From owner-chemistry@ccl.net Tue Nov  4 02:32:01 2008
From: "Orlin Blajiev blajiev*vub.ac.be" <owner-chemistry]^[server.ccl.net>
To: CCL
Subject: CCL: maximum displacement
Message-Id: <-38022-081103144647-16147-e6RBGAM9hA5D4m2gjiZ2kg]^[server.ccl.net>
X-Original-From: Orlin Blajiev <blajiev,+,vub.ac.be>
Date: Mon,  3 Nov 2008 20:14:15 +0100 (CET)


Sent to CCL by: Orlin Blajiev [blajiev%x%vub.ac.be]
Hi,

I will appreciate an advise how to relax  Maximum Displacement condition (or neglect it althogether). I am already using IOP(1/7=1200).

Maximum Force            0.000275     0.001800     YES
 RMS     Force            0.000063     0.001200     YES
 Maximum Displacement     0.125614     0.007200     NO 
 RMS     Displacement     0.017703     0.004800     NO 

Thank in advance.

Orlin

Orlin Blajiev
Electrochemical and Surface Engineering (SURF)
Faculty of Applied Science
Vrije Universiteit Brussel
Pleinlaan 2 - 1050 Brussels - Belgium
tel: ++32 2 6293538 - fax: ++32 2 6293200


From owner-chemistry@ccl.net Tue Nov  4 09:16:01 2008
From: "Qiang Fu qfu\a/kth.se" <owner-chemistry . server.ccl.net>
To: CCL
Subject: CCL: =?gb2312?B?tPC4tDogbWF4aW11bSBkaXNwbGFjZW1lbnQ=?=
Message-Id: <-38023-081104082646-31655-JPYcouHcfoDsO0iPV6jDKg . server.ccl.net>
X-Original-From: Qiang Fu <qfu()kth.se>
Content-Language: zh-CN
Content-Transfer-Encoding: base64
Content-Type: text/plain; charset="gb2312"
Date: Tue, 4 Nov 2008 13:54:16 +0100
MIME-Version: 1.0


Sent to CCL by: Qiang Fu [qfu=kth.se]
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From owner-chemistry@ccl.net Tue Nov  4 14:18:01 2008
From: "David Gallagher gallagher.da===gmail.com" <owner-chemistry]*[server.ccl.net>
To: CCL
Subject: CCL: MOPAC2009, new release, optimizes up to 15,000 atoms
Message-Id: <-38024-081104140639-17566-Jn78GjSk6F6u7fxt8xgXig]*[server.ccl.net>
X-Original-From: David Gallagher <gallagher.da%a%gmail.com>
Content-Type: multipart/alternative;
	boundary="=====================_16006531==.ALT"
Date: Tue, 04 Nov 2008 11:06:12 -0800
Mime-Version: 1.0


Sent to CCL by: David Gallagher [gallagher.da!=!gmail.com]
--=====================_16006531==.ALT
Content-Type: text/plain; charset="us-ascii"; format=flowed

MOPAC2009, new release, optimizes up to 15,000 atoms

The ability to model enzyme reactions, optimize whole proteins, 
segments of DNA, and other large systems is now available with the 
newly released MOPAC2009.

Conventional semiempirical quantum chemistry scales in both time and 
memory usage as the third power (cube) of the number of atoms, which 
sets the practical limit to about 1,000 atoms.  The linear scaling 
algorithm, MOZYME, now integrated into MOPAC2009, extends the size 
limit for geometry optimization to about 15,000 atoms, and for SCF to 
18,000 atoms, with dramatic increases in computational speed for any 
molecule larger than about 100 atoms.  With MOZYME, a molecule of 
1,000 atoms runs about 60 times faster and uses only 7% of the memory 
when compared to conventional MOPAC.

The keyword, MOZYME, works with most MOPAC functionality, including 
the new PM6 method which was parameterized primarily for biochemical 
systems.  MOPAC2009 is still free for academic non-profit use.  For 
further information please see: http://www.cacheresearch.com/mopac.html

David Gallagher
CACheResearch.com  
--=====================_16006531==.ALT
Content-Type: text/html; charset="us-ascii"

<html>
<body>
<b>MOPAC2009, new release, optimizes up to 15,000 atoms<br><br>
</b>The ability to model enzyme reactions, optimize whole proteins,
segments of DNA, and other large systems is now available with the newly
released MOPAC2009. <br><br>
Conventional semiempirical quantum chemistry scales in both time and
memory usage as the third power (cube) of the number of atoms, which sets
the practical limit to about 1,000 atoms.&nbsp; The linear scaling
algorithm, MOZYME, now integrated into MOPAC2009, extends the size limit
for geometry optimization to about 15,000 atoms, and for SCF to 18,000
atoms, with dramatic increases in computational speed for any molecule
larger than about 100 atoms.&nbsp; With MOZYME, a molecule of 1,000 atoms
runs about 60 times faster and uses only 7% of the memory when compared
to conventional MOPAC.&nbsp; <br><br>
The keyword, MOZYME, works with most MOPAC functionality, including the
new PM6 method which was parameterized primarily for biochemical
systems.&nbsp; MOPAC2009 is still free for academic non-profit use.&nbsp;
For further information please see:
<a href="http://www.cacheresearch.com/mopac.html" eudora="autourl">
http://www.cacheresearch.com/mopac.html<br><br>
</a>David Gallagher<br>
CACheResearch.com </body>
</html>

--=====================_16006531==.ALT--


From owner-chemistry@ccl.net Tue Nov  4 17:04:00 2008
From: "Kalju Kahn kalju=-=chem.ucsb.edu" <owner-chemistry-.-server.ccl.net>
To: CCL
Subject: CCL: maximum displacement
Message-Id: <-38025-081104162847-32246-qjY9DWTj4Oo28uXrBihlZg-.-server.ccl.net>
X-Original-From: "Kalju Kahn" <kalju(~)chem.ucsb.edu>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;charset=iso-8859-1
Date: Tue, 4 Nov 2008 13:28:28 -0800 (PST)
MIME-Version: 1.0


Sent to CCL by: "Kalju Kahn" [kalju+/-chem.ucsb.edu]
Orlin,

If you loosen these criteria too much, you will have a successful
calculation but the structure found will be too far from the true minimum.
 Being able to do a calculation is not the same thing as being able to get
the correct result.

If you really want to neglect displacement conditions, just use the
geometry that gave the results below (or pick a geometry with the lowest
energy from your search).

Your forces are small, the PES must be very flat in the region you are in:
large changes in the structure will cause only small change in energy.
You may want to make sure that your structure is a minimum, not a saddle
point or a some plateau via frequency calculation.  You should not have
negative frequencies.   After the frequency calculation, it will not hurt
to try Opt=ReadFC, Geom=Check; you might find a better structure quickly
using the correct Hessian.

Kalju

>
> Sent to CCL by: Orlin Blajiev [blajiev%x%vub.ac.be]
> Hi,
>
> I will appreciate an advise how to relax  Maximum Displacement condition
> (or neglect it althogether). I am already using IOP(1/7=1200).
>
> Maximum Force            0.000275     0.001800     YES
>  RMS     Force            0.000063     0.001200     YES
>  Maximum Displacement     0.125614     0.007200     NO
>  RMS     Displacement     0.017703     0.004800     NO
>
> Thank in advance.
>
> Orlin
>
> Orlin Blajiev
> Electrochemical and Surface Engineering (SURF)
> Faculty of Applied Science
> Vrije Universiteit Brussel
> Pleinlaan 2 - 1050 Brussels - Belgium
> tel: ++32 2 6293538 - fax: ++32 2 6293200>
>
>


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Kalju Kahn
Department of Chemistry and Biochemistry
UC Santa Barbara, CA 93106


From owner-chemistry@ccl.net Tue Nov  4 18:24:01 2008
From: "Carlos Abraham Diaz cancerbero_85%%hotmail.com" <owner-chemistry{:}server.ccl.net>
To: CCL
Subject: CCL: Question: arrhenius parameters with MOPAC
Message-Id: <-38026-081104161952-31315-c/bQH1w0iisW/OAe3pgUlQ{:}server.ccl.net>
X-Original-From: "Carlos Abraham Diaz" <cancerbero_85(~)hotmail.com>
Date: Tue, 4 Nov 2008 16:19:48 -0500


Sent to CCL by: "Carlos Abraham Diaz" [cancerbero_85|hotmail.com]
Hello. I need some help in the determination of the activation energy of this reaction:

  NH3  +      H3PO4         ------>   NH4H2PO4              +    H2O
ammonia   phosphoric acid           ammonium  phosphate        water

It's a neutralization and exothermic reaction. And however a fast raction rate (i can't measure with standard equipment) I assume that is a elementary reaction.

My questions are:

IT'S POSSIBLE CALCULATE THE Ea WITH MOPAC IN A NORMAL PC?
THERE IS NOT EXPERIMENTAL DATA ABOUT THIS REACTION?

I have the heats of formation of reagents and products and i tried the
bell-evans-polanyi correlation:

Ea = E* + BHf

And i found for a exothermic reaction that

Ea = 40 + 0.25Hf

But the result is a negative Ea.

I don't have so much knowledge in computational chemistry and i only need the numeric valor of the Ea and/or the reference.
Thank you.

Carlos Abraham Diaz
cancerbero_85===hotmail.com
Ciudad Obregon, Sonora, Mexico.


From owner-chemistry@ccl.net Tue Nov  4 18:59:01 2008
From: "alex Rudn rudikk99~~yahoo.com" <owner-chemistry(~)server.ccl.net>
To: CCL
Subject: CCL: GAMESS fatal error.
Message-Id: <-38027-081104162435-31782-LGhwaRQqKfwA6MVOuz86TA(~)server.ccl.net>
X-Original-From: "alex  Rudn" <rudikk99^^yahoo.com>
Date: Tue, 4 Nov 2008 16:24:31 -0500


Sent to CCL by: "alex  Rudn" [rudikk99^-^yahoo.com]
Dear CCLers, 

I tryed to parametrize heme using GAMESS. my input file is:
 
 $CONTRL RUNTYP=ENERGY $END
 $SYSTEM MEMORY=70000000 MEMDDI=2000000 $END
 $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 $END
 $ELPOT IEPOT=1 WHERE=PDC OUTPUT=BOTH $END
 $PDC PTSEL=CONNOLLY CONSTR=NONE PTDENS=1.6801711224 $END
 $CONTRL SCFTYP=RHF EXETYP=RUN MOLPLT=.TRUE. $END
 $STATPT NSTEP=100 $END
 $GUESS GUESS=HUCKEL $END
 $CONTRL COORD=ZMT NZVAR=219 ICHARG=0 MULT=1 $END
 $DATA
remark line goes here
C1
Fe1
N1       Fe1        b2
C1       N1         b3   Fe1        a3
C2       C1         b4   N1         a4   Fe1        t4
C3       C2         b5   C1         a5   N1         t5
N2       C3         b6   C2         a6   C1         t6
C4       N2         b7   C3         a7   C2         t7
C5       C4         b8   N2         a8   C3         t8
C6       C5         b9   C4         a9   N2         t9
N3       Fe1       b10   N1        a10   C1        t10
C7       N3        b11   Fe1       a11   N1        t11
C8       C7        b12   N3        a12   Fe1       t12
C9       C8        b13   C7        a13   N3        t13
N4       C9        b14   C8        a14   C7        t14
C10      N4        b15   C9        a15   C8        t15
C11      C10       b16   N4        a16   C9        t16
C12      N1        b17   Fe1       a17   N3        t17
C13      C12       b18   N1        a18   Fe1       t18
C14      C1        b19   N1        a19   Fe1       t19
C15      C14       b20   C1        a20   N1        t20
C16      C13       b21   C12       a21   N1        t21
C17      C16       b22   C13       a22   C12       t22
C18      C10       b23   N4        a23   C9        t23
C19      C9        b24   C8        a24   C7        t24
C20      C19       b25   C9        a25   C8        t25
C21      C20       b26   C19       a26   C9        t26
C22      C18       b27   C10       a27   N4        t27
C23      C7        b28   N3        a28   Fe1       t28
C24      C6        b29   C5        a29   C4        t29
C25      C24       b30   C6        a30   C5        t30
C26      C25       b31   C24       a31   C6        t31
C27      C26       b32   C25       a32   C24       t32
O1       C27       b33   C26       a33   C25       t33
O2       C27       b34   C26       a34   C25       t34
C28      C23       b35   C7        a35   N3        t35
C29      C4        b36   N2        a36   C3        t36
C30      C3        b37   C2        a37   C1        t37
C31      C30       b38   C3        a38   C2        t38
C32      C29       b39   C4        a39   N2        t39
C33      C32       b40   C29       a40   C4        t40
C34      C33       b41   C32       a41   C29       t41
O3       C34       b42   C33       a42   C32       t42
O4       C34       b43   C33       a43   C32       t43
H1       C2        b44   C1        a44   N1        t44
H2       C5        b45   C4        a45   N2        t45
H3       C8        b46   C7        a46   N3        t46
H4       C11       b47   C10       a47   N4        t47
H5       C15       b48   C14       a48   C1        t48
H6       C15       b49   C14       a49   C1        t49
H7       C15       b50   C14       a50   C1        t50
H8       C16       b51   C13       a51   C12       t51
H9       C17       b52   C16       a52   C13       t52
H10      C17       b53   C16       a53   C13       t53
H11      C20       b54   C19       a54   C9        t54
H12      C21       b55   C20       a55   C19       t55
H13      C21       b56   C20       a56   C19       t56
H14      C22       b57   C18       a57   C10       t57
H15      C22       b58   C18       a58   C10       t58
H16      C22       b59   C18       a59   C10       t59
H17      C25       b60   C24       a60   C6        t60
H18      C25       b61   C24       a61   C6        t61
H19      C26       b62   C25       a62   C24       t62
H20      C26       b63   C25       a63   C24       t63
H21      O2        b64   C27       a64   C26       t64
H22      C28       b65   C23       a65   C7        t65
H23      C28       b66   C23       a66   C7        t66
H24      C28       b67   C23       a67   C7        t67
H25      C31       b68   C30       a68   C3        t68
H26      C31       b69   C30       a69   C3        t69
H27      C31       b70   C30       a70   C3        t70
H28      C32       b71   C29       a71   C4        t71
H29      C32       b72   C29       a72   C4        t72
H30      C33       b73   C32       a73   C29       t73
H31      C33       b74   C32       a74   C29       t74
H32      O4        b75   C34       a75   C33       t75

b2= 2.0145
and so on
 $END
         After couple of hours of normal functioning it produces 
-cover page;
-modified input;
-table with atom, charge and x,y,z coordinates;
-mulliken and Lowdin Pop Anal;
-bond order and valevce Anal;
-electrostatic moments ; and then produce 
the next error msg:
           -----------------------
          ELECTROSTATIC POTENTIAL
          -----------------------

 POINT   X         Y         Z        ELECTRONIC     NUCLEAR       TOTAL
                (BOHR)                               (A.U.)
 MERZ-KOLLMAN RADII USED FOR CHARGE FITTING
          THE VDW RADIUS OF ATOMIC NUMBER 26IS UNKNOWN AND HAS BEEN SET TO1.80 ANGSTROMS
 MAXIMUM NUMBER OF POINTS MUST BE LESS THAN  10000
 EXECUTION OF GAMESS TERMINATED -ABNORMALLY- AT Tue Nov  4 00:45:35 2008
     4209387  WORDS OF DYNAMIC MEMORY USED
 STEP CPU TIME =    22.55 TOTAL CPU TIME =     4781.6 (   79.7 MIN)
 TOTAL WALL CLOCK TIME=    19555.8 SECONDS, CPU UTILIZATION IS  24.45%
 A fatal error occurred on DDI Process 0.
 ddikick.x: application process 0 quit unexpectedly.
 ddikick.x: Fatal error detected.
 The error is most likely to be in the application, so check for
 input errors, disk space, memory needs, application bugs, etc.
 ddikick.x will now clean up all processes, and exit...
 DDI Process 1: terminated upon request.
 ddikick.x: Sending kill signal to DDI processes.
 ddikick.x: Execution terminated due to error(s).
unset echo
----- accounting info -----
Tue Nov  4 00:45:38 EST 2008
Files used on the master node cumm044-0201-dhcp127.bu.edu were:
-rw-r--r-- 1 rudikk00 users     8725495 2008-11-04 00:45 .//a_1og2_crt_fe_mem.dat
-rw-r--r-- 1 rudikk00 users        7322 2008-11-03 19:19 .//a_1og2_crt_fe_mem.F05
-rw-r--r-- 1 rudikk00 users 44014627580 2008-11-03 19:33 .//a_1og2_crt_fe_mem.F08
-rw-r--r-- 1 rudikk00 users    41350648 2008-11-04 00:45 .//a_1og2_crt_fe_mem.F10
-rw-r--r-- 1 rudikk00 users        7322 2008-10-31 12:35 .//a_1og2_crt_fe_mem.inp
-rw-r--r-- 1 rudikk00 users     8129819 2008-11-04 00:45 .//a_1og2_crt_fe_mem.log
0.184u 2.868s 5:27:16.65 0.0%   0+0k 87120+24io 4pf+0w

the interesting observation is that after running that file I tryed to run  small files that I've already calculated earlier and all of them crashed immidiatly with the same error message. 

could somebode help me to get a clue what's wrong with this file and how to force it to work ferther and get it done? 

thank you very much in advance, 

Alex


From owner-chemistry@ccl.net Tue Nov  4 21:12:01 2008
From: "Gang Feng fegg7502]-[gmail.com" <owner-chemistry%a%server.ccl.net>
To: CCL
Subject: CCL: How to use p4vasp in windows XP
Message-Id: <-38028-081104210927-21091-eOuOlcAI9abrEM7eJVwdhg%a%server.ccl.net>
X-Original-From: "Gang  Feng" <fegg7502|a|gmail.com>
Date: Tue, 4 Nov 2008 21:09:24 -0500


Sent to CCL by: "Gang  Feng" [fegg7502%%gmail.com]
Dear All:

Guten tag!
I installed a P4vasp in the windows XP sp2 system on my PC yesterday, and I want to draw the DOS and PDOS with it. The problem is I can't open the DOSCAR with it. Also, when I open the vasprun.xml file it shows 'error reading property NAME' in the last line of its window. However, I could see the structure when opening the CHGCAR file.

Could anyone help me, please? Thank you very much in advance!!!


Best regards!
Yours sincerely!

Gang Feng
Email:fegg7502-#-gmail.com


From owner-chemistry@ccl.net Tue Nov  4 21:46:01 2008
From: "elite 158 elite158#%#gmail.com" <owner-chemistry^^^server.ccl.net>
To: CCL
Subject: CCL: Computational methods employed in drug discovery and generic drug development.
Message-Id: <-38029-081104213957-3111-+gvPTD+BhNPv7a0VJv4jRg^^^server.ccl.net>
X-Original-From: "elite 158" <elite158__gmail.com>
Content-Type: multipart/alternative; 
	boundary="----=_Part_50533_12598373.1225852785862"
Date: Wed, 5 Nov 2008 08:09:45 +0530
MIME-Version: 1.0


Sent to CCL by: "elite 158" [elite158++gmail.com]
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Dear CCLers,

Greetings and best wishes.

I am very keen to shape my career as a researcher in molecular modeling area
applied to pharmaceutical drug discovery and development through
computational methods.

My educational background (Bachelor in Pharmaceutical Sciences, India)
helped me understand subjects like medicinal chemistry, life sciences (from
the pharmacology point of view), and also basics of physical pharmacy (solid
state, thermodynamics etc).

I have a decent working knowledge in the implementation of computational
drug discovery methodologies like - Denovo, Structure based, Pharmacophore
and QSAR and I now seek to understand the computational methodologies
employed in drug development methodologies like - Virtual polymorph
screening and prediction, Analysis of powder X-ray diffraction data,
Morphology control, (Active Pharmaceutical Ingredient)-excipient
interactions, Simulation of delivery systems etc. Therefore I intend to
pursue a Masters / PhD program targeted towards these areas in
pharmaceutical domain.

Soon after, as a next step after Masters / PhD, I would also like to seek
education in the applications of nanotechnology in drug design and delivery.

I have been doing a lot of homework trying to identify Universities or
Research groups which have such programs. I would like to request you to
please help me identify any such programs / professors working in this
combined area across the globe if you know of any.

Any help is highly appreciated.

With warm regards,
Elite158.

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Dear CCLers, <br><br>Greetings and best wishes. <br><br>I am very keen to shape my career as a researcher in
molecular modeling area applied to pharmaceutical drug discovery and
development through computational methods. <br><br>My educational
background (Bachelor in Pharmaceutical Sciences, India) helped me understand subjects like medicinal chemistry, life
sciences (from the pharmacology point of view), and also basics of
physical pharmacy (solid state, thermodynamics etc). <br><br>I have a
decent working knowledge in the implementation of computational drug
discovery methodologies like - Denovo, Structure based, Pharmacophore
and QSAR and I now seek to understand the computational methodologies
employed in drug development methodologies like - Virtual polymorph
screening and prediction, Analysis of powder X-ray diffraction data,
Morphology control, (Active Pharmaceutical Ingredient)-excipient
interactions, Simulation of delivery systems etc. Therefore I intend to
pursue a Masters / PhD program targeted towards these areas in
pharmaceutical domain. <br><br>Soon after, as a next step after Masters / PhD, I
would also like to seek education in the applications of nanotechnology
in drug design and delivery.<br><br>I have been doing a lot of homework
trying to identify Universities or Research groups which have such programs. I would like
to request you to please help me identify any such programs /
professors working in this combined area across the globe if you know
of any. <br><br>Any help is highly appreciated.<br><br>With warm regards,<br>Elite158.<br>

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