From owner-chemistry@ccl.net Mon Dec 1 02:59:00 2008 From: "may abdelghani may01dz||yahoo.fr" To: CCL Subject: CCL: dative bonds Message-Id: <-38202-081130065541-19379-0mjyulirf3Zh8W4yEwMbzA() server.ccl.net> X-Original-From: may abdelghani Content-Type: multipart/alternative; boundary="0-979447664-1228046129=:64416" Date: Sun, 30 Nov 2008 11:55:29 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz*|*yahoo.fr] --0-979447664-1228046129=:64416 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear CCLers, How I=C2=A0=C2=A0know, theoretically, that this bond is a dative one. And w= itch atom is responsible on this dative behavior of this bond. =C2=A0=0A=0A=0A --0-979447664-1228046129=:64416 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable

Dear CCLers,

How I =  know, theoretically, that this bond is a dative one. An= d witch atom is= responsible on this dative behavior of this bond.= 

 

= =0A=0A=0A=0A --0-979447664-1228046129=:64416-- From owner-chemistry@ccl.net Mon Dec 1 05:22:00 2008 From: "Andrea Coletta andrea_coletta]~[libero.it" To: CCL Subject: CCL: OPLS parameters from Jorgensen Message-Id: <-38203-081201034556-13753-Z9TJZpS2khAePrFFiXvhmg ~ server.ccl.net> X-Original-From: Andrea Coletta Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 01 Dec 2008 09:45:47 +0100 MIME-Version: 1.0 Sent to CCL by: Andrea Coletta [andrea_coletta|libero.it] You can find the OPLS parameters in the GROMACS distribution... gromacs-*.*/share/top/ffoplsaa.* www.gromacs.org Anuradha Mittal amitta2.{:}.uic.edu ha scritto: > > Hi all, > > Are pepz database files (developed by Jorgensen) that contain OPLS > parameters for amino acids available for download anywhere? > > Thanks > Anu From owner-chemistry@ccl.net Mon Dec 1 06:29:01 2008 From: "Leyla Ramin l.ramin:_:aeromech.usyd.edu.au" To: CCL Subject: CCL: Ewald sum Message-Id: <-38204-081201062700-23125-nqkkuvMI1L6HN5S86lO+2Q]![server.ccl.net> X-Original-From: "Leyla Ramin" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C953A2.AA6DAA5C" Date: Mon, 1 Dec 2008 21:50:35 +1100 MIME-Version: 1.0 Sent to CCL by: "Leyla Ramin" [l.ramin-#-aeromech.usyd.edu.au] This is a multi-part message in MIME format. ------_=_NextPart_001_01C953A2.AA6DAA5C Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable =20 Hi everyone =20 I have recieved some result for my Ewald sum code, However I don't know = if they are correct or not. Can you please advise me how to evaluate my = results? =20 Regards Leyla Ramin ________________________________ > From: owner-chemistry+lram5228=3D=3Dusyd.edu.au-#-ccl.net on behalf of = Lukasz Cwiklik cwiklik.-#-.gmail.com Sent: Mon 01/12/2008 02:20 To: Leyla Ramin Subject: CCL: Ewald sum Sent to CCL by: "Lukasz Cwiklik" [cwiklik[*]gmail.com] On Sat, Nov 29, 2008 at 2:31 PM, Leila Ramin lram5228:-:usyd.edu.au wrote: > > Sent to CCL by: "Leila Ramin" [lram5228,usyd.edu.au] > Dear all, > > Can you please advise me in the Ewald sum method, in the loop over all = K vectors K=3D2*PI(kx/L,ky/L,kz/L) > why kx ranges over the values 0 to kmax only while ky and kz ranges = over > -Kmax,Kmax? Hi Leyla, If I understand correctly your question was addressed in the comment of the Allen's code: "IN ONE COORDINATE DIRECTION (X), SYMMETRY IS USED TO REDUCE ** C ** THE SUM TO INCLUDE ONLY POSITIVE K-VECTORS. ** C ** THE NEGATIVE VECTORS IN THIS DIRECTION ARE INCLUDED BY USE ** C ** OF THE MULTIPLICATIVE VARIABLE 'FACTOR'." Best, Lukasz -- Lukasz Cwiklik http://cwiklik.wordpress.com =20 -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml= =20Search Messages: http://www.ccl.net/htdig (login: ccl, Password: = search)http://www.ccl.net/spammers.txt------_=_NextPart_001_01C953A2.AA6DAA5C Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable CCL: Ewald sum=0A= =0A= =0A= =0A=
=0A=
 
=0A=
=0A=
Hi = everyone
=0A=
 
=0A=
I have recieved some result = for my Ewald sum code, However I don't know if they are correct or not. = Can you please advise me how to evaluate my results?
=0A=
 
=0A=
Regards
Leyla Ramin
=0A=

=0A=
=0A= From: = owner-chemistry+lram5228=3D=3Dusyd.edu.au-#-ccl.net on behalf of Lukasz = Cwiklik cwiklik.-#-.gmail.com
Sent: Mon 01/12/2008 = 02:20
To: Leyla Ramin
Subject: CCL: Ewald = sum

=0A=

=0A=

Sent to CCL by: "Lukasz Cwiklik" = [cwiklik[*]gmail.com]
On Sat, Nov 29, 2008 at 2:31 PM, Leila Ramin = lram5228:-:usyd.edu.au
<owner-chemistry*|*ccl.net> = wrote:
>
> Sent to CCL by: "Leila  Ramin" = [lram5228,usyd.edu.au]
> Dear all,
>
> Can you please = advise me in the Ewald sum method, in the loop over all K vectors = K=3D2*PI(kx/L,ky/L,kz/L)
> why kx ranges over the values 0 to kmax = only while ky and kz ranges over
> -Kmax,Kmax?


Hi = Leyla,
If I understand correctly your question was addressed in the = comment
of the Allen's code:
"IN ONE COORDINATE DIRECTION (X), = SYMMETRY IS USED TO REDUCE   **
C    ** THE = SUM TO INCLUDE ONLY POSITIVE = K-VECTORS.          &nb= sp;        **
C    = ** THE NEGATIVE VECTORS IN THIS DIRECTION ARE INCLUDED BY = USE    **
C    ** OF THE MULTIPLICATIVE = VARIABLE 'FACTOR'."

Best,
Lukasz


--
Lukasz = Cwiklik
http://cwiklik.wordpress.com


-=3D This is automatically added to each message by the = mailing script =3D-
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<= /BODY> ------_=_NextPart_001_01C953A2.AA6DAA5C-- From owner-chemistry@ccl.net Mon Dec 1 08:41:00 2008 From: "Andreas Klamt klamt^_^cosmologic.de" To: CCL Subject: CCL: COSMO-RS Symposium - 10 years of COSMOlogic Message-Id: <-38205-081201074337-20498-fCiHbvz5e6DiYC1IRTpWYQ]|[server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Mon, 01 Dec 2008 13:43:29 +0100 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt-#-cosmologic.de] Dear CCLers, hard to believe, but true: COSMOlogic is looking forward to its 10th anniversary on April 1, 2009. Quite exactly 10 years back from today I started to think about turning my developments on solvation models, i.e. COSMO and especially COSMO-RS, - which had grown as a byproduct of my comp. chem. work at Bayer - into a commercial enterprise, in order to be able to provide and further develop a most elaborate and scientificly sound tool for quantum chemically based solvation thermodynamics for academic and industrial computational chemists, chemical engineers, and pharmaceutical modellers. Many colleagues had been sceptic at that time, whether such enterprise could be successful, but now after 10 years we may conclude: Yes, it works! Thanks to all colleagues from academia and industry who have contributed to our success. We like to celebrate our birthday by a scientific COSMO-RS symposium, which shall give an overview of the extremely broad application range of COSMO-RS, ranging from chemical engineering solvent screening, via ionic liquids, pKa calculations, to the calculation of response properties in solution. Contributions by experienced users from academia and industry will be mixed with talks on the latest developments by our COSMOlogic team. The symposium will be surrounded by training courses for TURBOMOLE, COSMOtherm, and related tools from our COSMOlogic software suite and an anniversary banquette. We would be delighted to welcome many younger, as well as experienced computational chemists at our symposium. It will be a unique opportunity to learn most about the overwhelming importance of solvation in computational chemistry practice, and that COSMO-RS is much more than just COSMO, i.e. much more than a dielectric continuum solvation model. For more information see http://www.cosmologic.de/Symposium/symposium.html) Best regards on behalf of the entire COSMOlogic team Andreas Klamt -------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt]*[cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------- Please note our COSMO-RS Symposium in 2009 (For details see: http://www.cosmologic.de/Symposium/symposium.html) From owner-chemistry@ccl.net Mon Dec 1 09:15:01 2008 From: "Dongsheng Zhang zhdsheng21++gmail.com" To: CCL Subject: CCL: OPLS parameters from Jorgensen Message-Id: <-38206-081129220129-14607-ZteRtyTjOZbDEu9Fj/eUtQ%a%server.ccl.net> X-Original-From: "Dongsheng Zhang" Content-Type: multipart/alternative; boundary="----=_Part_36385_12675336.1228014076934" Date: Sat, 29 Nov 2008 21:01:16 -0600 MIME-Version: 1.0 Sent to CCL by: "Dongsheng Zhang" [zhdsheng21[]gmail.com] ------=_Part_36385_12675336.1228014076934 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Gromacs package has OPLS force field parameters. On Sat, Nov 29, 2008 at 5:53 PM, Anuradha Mittal amitta2.:_:.uic.edu < owner-chemistry:_:ccl.net> wrote: > > Hi all, > > Are pepz database files (developed by Jorgensen) that contain OPLS > parameters for amino acids available for download anywhere? > > Thanks > Anu > ------=_Part_36385_12675336.1228014076934 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Gromacs package has OPLS force field parameters.

On Sat, Nov 29, 2008 at 5:53 PM, Anuradha Mittal amitta2.:_:.uic.edu <owner-chemistry:_:ccl.net> wrote:

Hi all,

Are pepz database files (developed by Jorgensen) that contain OPLS parameters for amino acids available for download anywhere?

Thanks
Anu

------=_Part_36385_12675336.1228014076934-- From owner-chemistry@ccl.net Mon Dec 1 09:52:00 2008 From: "Tristan Youngs t.youngs##qub.ac.uk" To: CCL Subject: CCL: Ewald sum Message-Id: <-38207-081201094935-1707-pXn/U8kCPHb06EGaeoAIZg:+:server.ccl.net> X-Original-From: Tristan Youngs Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 01 Dec 2008 14:49:21 +0000 MIME-Version: 1.0 Sent to CCL by: Tristan Youngs [t.youngs()qub.ac.uk] You have several options: 1) Compare Ewald energies and forces for a simple system (e.g. of free atomic ions) calculated from your code against a 'trusted' other code - e.g. DL_POLY (against which the Ewald code in Aten was tested). 2) Compute a known figure such as the Madelung constant for sodium chloride, for example 3) You may always compute forces numerically from a series of Ewald energy calculations to see if your forces are correct, but only if you know the energy is correct in the first place! Tris. Leyla Ramin l.ramin:_:aeromech.usyd.edu.au wrote: > =20 > Hi everyone > =20 > I have recieved some result for my Ewald sum code, However I don't know= if they are correct or not. Can you please advise me how to evaluate my = results? > =20 > Regards > Leyla Ramin > > ________________________________ > > =20 >> From: owner-chemistry+lram5228=3D=3Dusyd.edu.au-x-ccl.net on behalf of= Lukasz Cwiklik cwiklik.-x-.gmail.com >> =20 > Sent: Mon 01/12/2008 02:20 > To: Leyla Ramin > Subject: CCL: Ewald sum > > > > > Sent to CCL by: "Lukasz Cwiklik" [cwiklik[*]gmail.com] > On Sat, Nov 29, 2008 at 2:31 PM, Leila Ramin lram5228:-:usyd.edu.au > wrote: > =20 >> Sent to CCL by: "Leila Ramin" [lram5228,usyd.edu.au] >> Dear all, >> >> Can you please advise me in the Ewald sum method, in the loop over all= K vectors K=3D2*PI(kx/L,ky/L,kz/L) >> why kx ranges over the values 0 to kmax only while ky and kz ranges ov= er >> -Kmax,Kmax? >> =20 > > > Hi Leyla, > If I understand correctly your question was addressed in the comment > of the Allen's code: > "IN ONE COORDINATE DIRECTION (X), SYMMETRY IS USED TO REDUCE ** > C ** THE SUM TO INCLUDE ONLY POSITIVE K-VECTORS. *= * > C ** THE NEGATIVE VECTORS IN THIS DIRECTION ARE INCLUDED BY USE *= * > C ** OF THE MULTIPLICATIVE VARIABLE 'FACTOR'." > > Best, > Lukasz > > > -- > Lukasz Cwiklik > http://cwiklik.wordpress.com =20 > > > > -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/che= mistry/sub_unsub.shtml Search Messages: http://www.c= cl.net/htdig (login: ccl, Password: search)http://www.ccl.net/spammers.t= xt------_=3D_NextPart_001_01C953A2.AA6DAA5C > Content-Type: text/html; > charset=3D"iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > CCL: Ewald sum > > > >
>
 = ;
>
>
Hi everyone<= /FONT>
>
 
>
I have recieved some result = for my Ewald sum code, However I don't know if they are correct or not. C= an you please advise me how to evaluate my results?
>
 
>
Regards
Leyla Ramin
>

>
> From: owner-chemistry+lram5228=3D=3D= usyd.edu.au-x-ccl.net on behalf of Lukasz Cwiklik cwiklik.-x-.gmail.comSent: Mon 01/12/2008 02:20
To: Leyla Ramin
Subje= ct: CCL: Ewald sum

>

>

Sent to CCL by: "Lukasz Cwiklik" [cwiklik[*]gmail.com= ]
On Sat, Nov 29, 2008 at 2:31 PM, Leila Ramin lram5228:-:usyd.edu.au<= BR><owner-chemistry*|*ccl.net> wrote:
>
> Sent to CCL b= y: "Leila  Ramin" [lram5228,usyd.edu.au]
> Dear all,
>> Can you please advise me in the Ewald sum method, in the loop over= all K vectors K=3D2*PI(kx/L,ky/L,kz/L)
> why kx ranges over the va= lues 0 to kmax only while ky and kz ranges over
> -Kmax,Kmax?

Hi Leyla,
If I understand correctly your question was addressed = in the comment
of the Allen's code:
"IN ONE COORDINATE DIRECTION (X= ), SYMMETRY IS USED TO REDUCE   **
C    ** TH= E SUM TO INCLUDE ONLY POSITIVE K-VECTORS.     &n= bsp;           &nb= sp; **
C    ** THE NEGATIVE VECTORS IN THIS DIRECTION A= RE INCLUDED BY USE    **
C    ** OF THE = MULTIPLICATIVE VARIABLE 'FACTOR'."

Best,
Lukasz


--Lukasz Cwiklik
http://cwik= lik.wordpress.com



-=3D This is automatically added to = each message by the mailing script =3D-
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If your mail bounces fr= om CCL with 5.7.1 error, check:
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> =20 --=20 Dr. T. Youngs (t.youngs\a/qub.ac.uk) Atomistic Simulation Centre Old Physics Building Queen's University Belfast Belfast, BT7 1NN, N.I. From owner-chemistry@ccl.net Mon Dec 1 10:26:01 2008 From: "Mahmoud Korani Abdel-Latif mkkhedr a hotmail.com" To: CCL Subject: CCL: XYZ Coordinate Shift Message-Id: <-38208-081201095121-3157-NQrXYbYpA99BcMtNbUF9Vg]_[server.ccl.net> X-Original-From: "Mahmoud Korani Abdel-Latif" Date: Mon, 1 Dec 2008 09:51:17 -0500 Sent to CCL by: "Mahmoud Korani Abdel-Latif" [mkkhedr|-|hotmail.com] Dear CCLer's I have the XYZ for certain molecule and I need to shift this XYZ to certain values. What I need is that "I need no negative values in the XYZ" because I need that positive coordinates in other calculations. Is any free program that can do that? Is any script for doing that? Any help to do the above issue will be greatly appreciated. Thanks in advance Mahmoud From owner-chemistry@ccl.net Mon Dec 1 12:14:00 2008 From: "Close, David M. CLOSED|,|mail.etsu.edu" To: CCL Subject: CCL: XYZ Coordinate Shift Message-Id: <-38209-081201120723-23546-Ocq90GxDTFY3wIVwdEnyEg-.-server.ccl.net> X-Original-From: "Close, David M." Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Mon, 1 Dec 2008 10:44:52 -0500 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED[*]mail.etsu.edu] Mahmoud: I would ask a crystallographer for help. They can show you how to graph your xyz coordinates in the unit cell. If some parts of a particular molecule are outside the unit cell, you could just increase the unit cells dimensions. =20 Of course crystallographers use fractional coordinates. That's just x/a, y/b, z/c, etc. You can easily transform these back to xyz coordinates with BABEL. Regards, Dave Close From owner-chemistry@ccl.net Mon Dec 1 13:34:01 2008 From: "Warren DeLano warren^_^delsci.com" To: CCL Subject: CCL: XYZ Coordinate Shift Message-Id: <-38210-081201131943-16945-vTNadJya0LVsAKS95FiKMQ#server.ccl.net> X-Original-From: "Warren DeLano" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="US-ASCII" Date: Mon, 1 Dec 2008 09:46:50 -0800 MIME-Version: 1.0 Sent to CCL by: "Warren DeLano" [warren::delsci.com] PyMOL does this sort of thing pretty easily: load old_file.pdb alter_state 1, all, (x,y,z)=3D(x+10,y+2,z+8)=20 save new_file.pdb This capability has been present for years, so the obsolete free builds wills suffice: http://delsci.com/rel/099 Cheers, Warren -----Original Message----- > From: owner-chemistry+warren=3D=3Ddelsci.com*_*ccl.net [mailto:owner-chemistry+warren=3D=3Ddelsci.com*_*ccl.net] On Behalf Of = Mahmoud Korani Abdel-Latif mkkhedr a hotmail.com Sent: Monday, December 01, 2008 8:27 AM To: Warren DeLano Subject: CCL: XYZ Coordinate Shift Sent to CCL by: "Mahmoud Korani Abdel-Latif" [mkkhedr|-|hotmail.com] Dear CCLer's I have the XYZ for certain molecule and I need to shift this XYZ to certain values. What I need is that "I need no negative values in the XYZ" because I need that positive coordinates in other calculations. =20 Is any free program that can do that? Is any script for doing that? Any help to do the above issue will be greatly appreciated. Thanks in advance=20 Mahmoud -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Dec 1 14:12:01 2008 From: "Daniel Jana dfjana^_^gmail.com" To: CCL Subject: CCL: XYZ Coordinate Shift Message-Id: <-38211-081201134414-25040-F/VE7DwBkAJoQ93iOifhDQ^server.ccl.net> X-Original-From: Daniel Jana Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 01 Dec 2008 19:44:00 +0100 MIME-Version: 1.0 Sent to CCL by: Daniel Jana [dfjana : gmail.com] Mahmoud Korani Abdel-Latif mkkhedr a hotmail.com wrote: > Sent to CCL by: "Mahmoud Korani Abdel-Latif" [mkkhedr|-|hotmail.com] > Dear CCLer's > I have the XYZ for certain molecule and I need to shift this XYZ to certain values. What I need is that "I need no negative values in the XYZ" because I need that positive coordinates in other calculations. > > Is any free program that can do that? > > Is any script for doing that? > A XYZ file is just a text file with a number on the first line (the number of atoms) a free format line and then a list of atoms with respective XYZ coordinates (4 columns per line). If you take the coordinates from the file, put them in a spreadsheet program (Office, OpenOffice, Gnumeric) and then sum to each element a number (one value for all) big enough to make all of them positive, you get the desired behavior. Then you copy that back into a xyz file and there you go, you have everything positive. This is time consuming but beats learning a new program just to do that. In case you are using Linux, I just cooked up something for you. awk 'a=10 { if (FNR <= 2) print ; else printf("%2s %11.6f %11.6f %11.6f \n",$1,$2+a,$3+a,$4+a) }' All of this should be done in one line in the shell (from awk to ). should be the name of your xyz file. The parameter in beginning (the a=10) is the shift of positions (in this case, 10 Angstrom). Substitute that by any value (integer or not, a decimal number will use a . [9.5 for instance]) and you'll get the corresponding shift. The shift will be done equally in all dimensions. I only tried this in a couple of files and one operating system but it should work on any linux and with any correctly done XYZ file that contains only one structure. Best regards, Daniel Jana PS - This can easily be put on a shell script to avoid having to memorize (or copy and paste) all of that. But I think this mail is long enough... From owner-chemistry@ccl.net Mon Dec 1 15:14:00 2008 From: "Deskins, Nathaniel A nathaniel.deskins^pnl.gov" To: CCL Subject: CCL: XYZ Coordinate Shift Message-Id: <-38212-081201150733-25028-ZYTHldgG3BcBP2czlrZ18Q~~server.ccl.net> X-Original-From: "Deskins, Nathaniel A" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Mon, 1 Dec 2008 11:07:16 -0800 MIME-Version: 1.0 Sent to CCL by: "Deskins, Nathaniel A" [nathaniel.deskins .. pnl.gov] You could do this very easily (I routinely do) using a spreadsheet program like Excel. You just have to be careful with tab characters versus spaces. I copy or open the coordinates in Excel, manipulate the values (e.g. add 10 to every x value), then copy the results into a text file. I then open the file with Vi and "1,$s/^I/ /g" removes tabs and replaces them with spaces. Note that "^I" is ctrl-V followed by the tab button (at least in Windows). Aaron -----Original Message----- Sent to CCL by: "Mahmoud Korani Abdel-Latif" [mkkhedr|-|hotmail.com] Dear CCLer's I have the XYZ for certain molecule and I need to shift this XYZ to certain values. What I need is that "I need no negative values in the XYZ" because I need that positive coordinates in other calculations. =20 Is any free program that can do that? Is any script for doing that? Any help to do the above issue will be greatly appreciated. Thanks in advance=20 Mahmoud From owner-chemistry@ccl.net Mon Dec 1 17:45:01 2008 From: "Tris Youngs t.youngs[a]qub.ac.uk" To: CCL Subject: CCL: XYZ Coordinate Shift Message-Id: <-38213-081201171959-5834-vk2XExuF1aDtxn+7Szt6Ig]^[server.ccl.net> X-Original-From: Tris Youngs Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Mon, 1 Dec 2008 21:43:09 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: Tris Youngs [t.youngs,+,qub.ac.uk] I would hate to overload you with solutions, but Aten (www.projectaten.org, get the Beta version) will also do what you want. For example, from the command line one could do: > aten old.xyz -c 'selectall; translate 10 10 10; savemodel xyz new.xyz; quit' ...to translate all coordinates by 10 Angstroms in each direction. If you want all coordinates moved to the 'lower left-hand corner' you can find the extreme lower-left-hand coordinate first: > aten old.xyz -c 'real minx,miny,minz; atom i; $minx = 1000.0; $miny = 1000.0; $minz = 1000.0; for $i; if $i.rx < $minx; $minx = $i.rx; end; if $i.ry < $miny; $miny = $i.ry; end; if $i.rz < $minz; $minz = $i.rz; end; end; print "Translation is $minx $miny $minz"; selectall; translate -$minx -$miny -$minz; savemodel xyz new.xyz; quit' It is also easy with the --batch command to do this for multiple files at once. Hope this helps! Tris. -- Dr. T. Youngs (t.youngs~!~qub.ac.uk) Atomistic Simulation Centre Old Physics Building Queen's University Belfast Belfast, BT7 1NN, N.I. From owner-chemistry@ccl.net Mon Dec 1 20:06:00 2008 From: "S. B. Bill S_Bill36||yahoo.co.uk" To: CCL Subject: CCL: PDB file modification for AMBER Message-Id: <-38214-081201123016-32586-BD4hHRCAZ8uGtGeniPptCA]~[server.ccl.net> X-Original-From: "S. B. Bill" Date: Mon, 1 Dec 2008 12:30:13 -0500 Sent to CCL by: "S. B. Bill" [S_Bill36#%#yahoo.co.uk] Dear users I have a couple of questions related to pdb file modification before usage in amber and I hope you help me. How can I now the histidine residue in the pdb file is delta-poistion protonated or epsilon position? How can I now that the cysteine residue inovlved in disulphide bridge or not? Also, is the any other modification should I do before usage the pdb file in Amber rather than deleting water molecules and editing Cysteine and Hisitidine? Ohh, sorry, there are a rows called "Connect" at the end of the pdb file, should I delet these rows and I am going to use it an how? One mor equestion, HETATM row means this residue is a non-standard residue. But, I have a strange file, for the same residue, he said one time it is ATOM, and another time it is a HETATM, as can you see below, why? ATOM 1839 N SER A 260 1.478 57.001 -12.410 1.00 35.40 N HETATM 1845 N SEP A 261 4.705 58.147 -11.356 1.00 44.70 N Sorry, but I have another question, say the file said the file contains two HETATM VRV residues with different serial number, in this case, should I paramaterize this VRV two time, or just one time? if one time, which coordinates should I use, of the first one or the second one? In fact, I need answer for my question ASAP. Thanks in advance From owner-chemistry@ccl.net Mon Dec 1 20:40:01 2008 From: "Mihaly Mezei Mihaly.Mezei(~)mssm.edu" To: CCL Subject: CCL: Ewald sum Message-Id: <-38215-081201112543-1129-ftt05wRCgZlsCLnZiESSCQ|*|server.ccl.net> X-Original-From: Mihaly Mezei Content-disposition: inline Content-language: en Content-transfer-encoding: 7BIT Content-type: text/plain; charset=us-ascii Date: Mon, 01 Dec 2008 09:57:51 -0500 MIME-version: 1.0 Sent to CCL by: Mihaly Mezei [Mihaly.Mezei-,-mssm.edu] > I have recieved some result for my Ewald sum code, However I don't > know if they are correct or not. Can you please advise me how to > evaluate my results? > Onesuch test is that the result should be the same with different weights given to the direct and reciprocal spacecontribution. Mihaly Mezei Department of Structural and Chemical Biology, Mount Sinai School of Medicine, NYU Voice: (212) 659-5475 Fax: (212) 849-2456 WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632 WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei WWW (Department): http://atlas.physbio.mssm.edu From owner-chemistry@ccl.net Mon Dec 1 21:47:01 2008 From: "Brunsteiner, Michael micb|uic.edu" To: CCL Subject: CCL: PDB file modification for AMBER Message-Id: <-38216-081201214541-23943-uF/iNo5GcWLCce+QB+dQNQ]=[server.ccl.net> X-Original-From: "Brunsteiner, Michael" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 1 Dec 2008 20:45:23 -0600 (CST) MIME-Version: 1.0 Sent to CCL by: "Brunsteiner, Michael" [micb[A]uic.edu] On Mon, December 1, 2008 11:30, S. B. Bill S_Bill36||yahoo.co.uk wrote: > > Sent to CCL by: "S. B. Bill" [S_Bill36#%#yahoo.co.uk] > Dear users > I have a couple of questions related to pdb file modification before usage > in amber and I hope you help me. > How can I now the histidine residue in the pdb file is delta-poistion > protonated or epsilon position? depends on how many structures you have to process ... if only a few you can do it through visual inspection in some viewer like chimera or vmd, by optimizing hydrogen bonds. if you have many structures you better use a program like reduce or whatif (google for these) > How can I now that the cysteine residue inovlved in disulphide bridge or > not? the above programs (and others) might do that too, but i am not sure - again, if you have only one or a few structures do visual inspection ... > Also, is the any other modification should I do before usage the pdb file > in Amber rather than deleting water molecules and editing Cysteine and > Hisitidine? check all ionizable amino acids. and check whether some GLN, ASN or HIS need to be flipped (reduce or nq-flipper) and of course you will have to adjust residue names and atom names/order unless some program (antechamber?) does that for you ... also if there's any ions in your structure you might want to keep those, the same goes for conserved water molecules that might mediate receptor-ligand interactions in case there is a ligand ... > Ohh, sorry, there are a rows called "Connect" at the end of the pdb file, > should I delet these rows and I am going to use it an how? those for the protein you can delete, if you have any ligands in there you either remove them, or use gaff in combination with leap/antechamber, then the CONNECT records might be useful ... look at the amber docs ... > One mor equestion, HETATM row means this residue is a non-standard > residue. But, I have a strange file, for the same residue, he said one > time it is ATOM, and another time it is a HETATM, as can you see below, > why? > ATOM 1839 N SER A 260 1.478 57.001 -12.410 1.00 35.40 > N > HETATM 1845 N SEP A 261 4.705 58.147 -11.356 1.00 44.70 > N its actually NOT the same residue, the residue name of ATOM 1839 is SER (which is serine, an amino aicd, therefore its an ATOM, the other one has SEP, which is not a standard amino acid residue name, therefore its a hetero-atom (HETATM)) > Sorry, but I have another question, say the file said the file contains > two HETATM VRV residues with different serial number, in this case, should > I paramaterize this VRV two time, or just one time? if one time, which > coordinates should I use, of the first one or the second one? > In fact, one time, if its really the same compound, and then it also shouldn't matter which one you take ... but i am not sure i understood your question correctly. one more thing: none of the programs mentioned above is completely foolproof, so if you want to make sure to get a decent input structure always check it by visual inspection before using it ... > I need answer for my question ASAP. ... considering the questions you asked you don't seem to have too much experience in these things, but this is something you cannot easily learn in a couple of days, there's numerous pitfalls. If I was you I'd take my time and at least work through a couple of tutorials before setting up and starting any lengthy simulations. If you do things in a rush you may end up being a very sad person who did a lot of work only to produce a nice collection of irreproducible artifacts ;) good luck! michael