Yes=2C have a look at:

Mohammad Mehdi Ghahremanpour=2C Seyed Shahriar Arab=2C Saman Biook Agha= zadeh=2C Jin Zhang and David van der Spoel:=0A= MemBuilder: A Web-Based Graphical Interface to =0A= Build Heterogeneously Mixed Membrane Bilayers for the GROMACS =0A= Biomolecular Simulation Program=0A= Bioinformatics 30 pp. 439-441 (2014)

Sergio
<= br>

From: owner-chemistry]^[ccl.netTo: sergio.manzetti]^[gmx.com
Subject: CCL: Membrane building tools
Da= te: Mon=2C 10 Mar 2014 09:21:12 -0500

=0A= =0A= =0A=

Does anybody know of a reliable tool to build a cell membr= ane that is larger than say 100 by 100 lipids per leaf? =3BI've tried = the CHARMM gui and CELLmicrocosmos MembraneEditor=2C but neither work for m= y purpose. =3BI can build something that has 300 or 400 lipids per lea= f=2C but I'd like something larger than that (if possible). =3BWho kno= ws=2C something as big as I want may not have been done before.

TIA=2C

Richard

= --_cca8ac83-3c18-4859-a936-8b4fccd4546b_-- From owner-chemistry@ccl.net Tue Mar 11 01:02:00 2014 From: "Jernej Zidar jernej.zidar*gmail.com" To: CCL Subject: CCL: Membrane building tools Message-Id: <-49829-140310212856-9762-Gd1Sc2wf+Tw5PmKMPvo9fA||server.ccl.net> X-Original-From: Jernej Zidar Content-Type: text/plain; charset=UTF-8 Date: Tue, 11 Mar 2014 09:28:50 +0800 MIME-Version: 1.0 Sent to CCL by: Jernej Zidar [jernej.zidar,gmail.com] I would build a small membrane leaflet and the replicate this segment in the x-y plane. This is trivial both in CHARMM and Gromacs. Best, Jernej On Tue, Mar 11, 2014 at 12:39 AM, Felipe Pineda pideca,hotmail.com wrote: > Have you also tried packmol (http://www.ime.unicamp.br/~martinez/packmol/)? > > Good luck! > > Felipe > > > ________________________________ > From: owner-chemistry * ccl.net > To: fpineda * uni-bonn.de > Subject: CCL: Membrane building tools > Date: Mon, 10 Mar 2014 09:21:12 -0500 > > > Does anybody know of a reliable tool to build a cell membrane that is larger > than say 100 by 100 lipids per leaf? I've tried the CHARMM gui and > CELLmicrocosmos MembraneEditor, but neither work for my purpose. I can > build something that has 300 or 400 lipids per leaf, but I'd like something > larger than that (if possible). Who knows, something as big as I want may > not have been done before. > > TIA, > Richard > > -- Windows: Re-Boot, Linux: Be-Root. From owner-chemistry@ccl.net Tue Mar 11 02:48:01 2014 From: "Van Dam, Hubertus J HubertusJJ.vanDam^^^pnnl.gov" To: CCL Subject: CCL: NwChem onion error with MCSCF as high Message-Id: <-49830-140311024513-15254-5vBbgeakeRbjvL0rj+mtcA|server.ccl.net> X-Original-From: "Van Dam, Hubertus J" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 11 Mar 2014 06:45:06 +0000 MIME-Version: 1.0 Sent to CCL by: "Van Dam, Hubertus J" [HubertusJJ.vanDam-.-pnnl.gov] Hi Tudor, Thank you for reporting this issue. I have been able to reproduce your problem and identified the root cause. You specify in the oniom block high MCSCF basis high but the code does not recognize the theory "MCSCF". If you replace this line with high mcscf basis high then this problem should be solved. Obviously the theory string should be case insensitive and I will check a fix in for this. In the meantime this workaround should get you going. Please let me know if you encounter any other issues. Best wishes, Huub van Dam Pacific Northwest National Laboratory Tel: 509-372-6441 -----Original Message----- > From: owner-chemistry+hubertus.vandam==pnnl.gov _ ccl.net [mailto:owner-chemistry+hubertus.vandam==pnnl.gov _ ccl.net] On Behalf Of Tudor Spataru ts2407#%#columbia.edu Sent: Friday, March 07, 2014 8:25 AM To: Van Dam, Hubertus J Subject: CCL: NwChem onion error with MCSCF as high Sent to CCL by: "Tudor Spataru" [ts2407**columbia.edu] Dear All, I am trying to run an oniom calculations with MCSCF as a high theory (model) and DFT (B3LYP) as a low theory(real). DFT it seems to work perfectly, while MCSCF is not running. This is strange taking into account that absolutely the same MCSCF options and the same keywords in separate calculations are running perfectly, while in onion not. The copy of the error is here: ONIOM HIGH+MODEL ---------------- task_gradient: unknown theory 0 ------------------------------------------------------------------------ There is an error in the input file ------------------------------------------------------------------------ For more information see the NWChem manual at http://www.nwchem-sw.org/index.php/NWChem_Documentation For further details see manual section: My file is here: title "baseon_initial" start baseon_initial charge -1 geometry units angstroms noautoz N -0.95397587 2.95740479 2.14169265 Co -1.03175053 3.95352527 0.28303474 N -0.38447491 3.65785155 -1.66657841 N -2.21192196 2.39508772 -0.36274893 C -1.84045646 2.04779587 2.51818735 C 1.35860107 4.98010449 1.90036474 C 0.87047059 4.35233977 3.05589061 C 2.51269852 5.97500658 1.82560352 H 1.36754534 4.61847968 3.97580650 C -0.16352515 3.41817832 3.18262110 C -0.57305121 2.71306962 4.47227292 C -1.80654069 1.88233294 4.04001994 H -2.72170924 2.28737168 4.46293739 C -2.70809155 1.30806410 1.70285982 C -2.81154287 1.46132430 0.30185479 C -3.66954394 0.60040921 -0.64267787 C -3.10359966 1.00147846 -2.03807378 H -2.32655156 0.30061412 -2.33271601 C -2.48909045 2.40447671 -1.79251906 H -3.23492907 3.17507056 -1.98481837 C -1.33546028 3.67539117 -3.81663807 C -0.06294607 4.56355531 -3.79078836 H -0.24520733 5.56482355 -4.16385491 C 0.29319528 4.57555496 -2.30333868 C 1.46986654 5.47877863 -0.30523312 C 1.19869335 5.45592892 -1.68822415 C 2.50688690 6.40291319 0.33403454 H 2.37263205 6.81538270 2.49687104 N 0.86228799 4.77227986 0.63083794 H -0.63320033 1.89564143 -2.77048337 H -4.69363885 0.96171637 -0.55238706 C -1.18841530 2.80575101 -2.54186546 H -2.21431594 4.30456789 -3.71737654 H -1.43261212 3.10121764 -4.73217754 H 0.74338252 4.13406365 -4.37974542 H 1.71340665 6.17245181 -2.30327363 H 3.47947035 6.30505776 -0.13489209 H 2.19330702 7.43586015 0.21602934 H 3.45452923 5.50297071 2.09688761 H -0.80453276 3.41703098 5.26506045 H 0.22817464 2.07405164 4.83765996 H -3.33065865 0.57838713 2.18759855 H -1.74767248 0.84204759 4.33643676 H -3.86132794 0.99791812 -2.81651531 C -2.43197524 5.60816783 0.38515618 H -2.24651519 6.31045295 1.20925468 H -2.43806326 6.21157090 -0.53467763 H -3.45960867 5.24137404 0.51556660 C 3.98033352 -1.40218052 -0.24335612 C 1.82017412 -1.13383339 0.28426693 C 3.59760420 -0.05775958 -0.29207224 C 5.27393835 -1.78243595 -0.55833895 H 0.82739488 -1.39262230 0.56624814 C 4.50076642 0.93568429 -0.64473118 C 6.20552946 -0.79060708 -0.93017179 H 5.57517275 -2.81594412 -0.52984110 C 5.81826899 0.57699251 -0.97035742 H 4.17859666 1.96062820 -0.66733614 N 2.83030457 -2.10002815 0.15569324 N 2.25833416 0.06563919 0.04308170 C 7.58417734 -1.26146775 -1.34301956 H 7.95454622 -2.01797712 -0.65843635 H 7.55050657 -1.70518137 -2.33550184 H 8.30967452 -0.46119959 -1.36931559 C 6.73561105 1.70261967 -1.40284381 H 6.59410301 1.93962749 -2.46065935 H 6.51168627 2.59591566 -0.83270806 H 7.78772075 1.48041267 -1.25458450 O -0.85535110 -7.40167032 0.74784510 H -0.66471362 -8.16152636 0.20957727 C -3.65510720 -0.89399250 -0.30923488 H -3.69820898 -1.00356968 0.76342243 H -2.71834804 -1.33114738 -0.63870809 C -4.83487107 -1.70198377 -0.90432345 H -4.62446746 -1.99409882 -1.92597800 H -5.73128916 -1.09599421 -0.90327474 C -5.10575232 -2.89461117 -0.01835989 O -5.55712215 -2.76047750 1.09964193 N -4.77233827 -4.12678292 -0.49908035 H -4.40312008 -4.20638367 -1.42742247 C -4.74650016 -5.27284060 0.38592480 H -5.67766013 -5.83395584 0.35390153 H -4.63904964 -4.89061061 1.39078620 C -3.61431926 -6.24625772 0.06571528 H -3.57436405 -6.98777202 0.85997411 C -3.78743560 -6.94873392 -1.28098431 H -3.77730327 -6.24065263 -2.10077759 H -3.00073370 -7.66523045 -1.47186126 H -4.72934631 -7.47680598 -1.27934736 O -2.37041832 -5.49291136 0.13850719 P -0.96600039 -6.09437209 -0.17397115 O -0.01928817 -5.04353376 0.50786757 O -0.67306817 -6.43829764 -1.55903299 C 2.73713344 -3.46885178 0.37109204 O 2.72741750 -4.28822686 -0.74041447 C 1.98203330 -4.10855650 1.51809215 C 2.20268414 -5.57597270 -0.39578290 C 1.34192215 -5.34686174 0.86008987 H 2.69856078 -4.46489428 2.25060542 H 1.59721370 -5.90122657 -1.22419002 H 1.33372240 -6.19522078 1.53039218 C 3.35578452 -6.54153898 -0.19203223 H 3.88770496 -6.65050502 -1.12699573 H 2.98168460 -7.51702031 0.09740551 O 4.23902136 -6.11586096 0.83613828 H 4.73620217 -5.37162090 0.50901011 O 1.01886991 -3.30779790 2.14989057 H 1.45933418 -2.66194209 2.68695155 end basis high C library "6-31G" H library "6-31G" Co library "6-31G**" N library "6-31G" end basis low C library "6-31G**" H library "6-31G" P library "6-31G**" O library "6-31G**" N library "6-31G**" Co library "6-31G**" end MCSCF multiplicity 2 ACTIVE 13 ACTELEC 13 maxiter 1999 END dft iterations 1999 mult 2 xc b3lyp end oniom low dft basis low high MCSCF basis high model 60 charge 0 16 71 0.709 55 61 0.709 57 65 0.709 59 94 0.766 end task oniom optimize Best wishes, Tudor My name is: Tudor Spataru, my e-mail address is: ts2407 .. columbia.eduhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Mar 11 07:24:00 2014 From: "Zakieh Yousefi zakiehyousefi*o*yahoo.com" To: CCL Subject: CCL: Fukui function Message-Id: <-49831-140311071935-12647-VhNmGboHLN930wKmeW9Pfg[a]server.ccl.net> X-Original-From: "Zakieh Yousefi" Date: Tue, 11 Mar 2014 07:19:34 -0400 Sent to CCL by: "Zakieh Yousefi" [zakiehyousefi^-^yahoo.com] Dear All, I'm going to compute fukui indices of some organic ligand. I compute natural bond charges of each condensed atom with N, N+1 and N-1 electrons.Then, condensed charges must be replaced in follwed formula: F+(K)=qk(N-1)-q(k) Now, I want to know I locate a value of charge without sign or with it for example if a charge of atom would be -0.5, we must locate 0.5 or -0.5 in formula. I need your kind helps. Best Yousefi Ferdowsi university of Mashhad Mashhad Iran zakiehyousefi(0)yahoo.com From owner-chemistry@ccl.net Tue Mar 11 07:59:00 2014 From: "=?ISO-8859-1?Q?Bj=F6rn_Sommer?= bjoern * CELLmicrocosmos.org" To: CCL Subject: CCL: Membrane building tools Message-Id: <-49832-140311064945-10947-n0OlqXn2RMUKM7DSWvAiIg---server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Bj=F6rn_Sommer?= Content-type: multipart/alternative; boundary="Boundary_(ID_q07+Rfl24XdTA/UnOl8mEQ)" Date: Tue, 11 Mar 2014 11:49:33 +0100 MIME-version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Bj=F6rn_Sommer?= [bjoern-,-CELLmicrocosmos.org] This is a multi-part message in MIME format. --Boundary_(ID_q07+Rfl24XdTA/UnOl8mEQ) Content-type: text/plain; charset=ISO-8859-1; format=flowed Content-transfer-encoding: 8BIT Richard, the MembraneEditor is able to handle also larger membranes, but make sure that 1) you use a 64 bit machine and 2) you use a 64 bit Java version. With 32 bit you are completely right: this will not work. If you are a user of Eclipse, you can also just download and import the project into your workspace from here: http://cellmicrocosmos.org/index.php/download In this case, do not forget to install Java 3D on your machine: http://java3d.java.net For your purpose, I would suggest two workflows: 1.) Easy: Define a membrane size of ca. 800x800, maybe a little bit larger. Use the Distributor algorithm. Type as Lipids EC 10,000 and Lipids IC 10,000 and press "Apply counts". Wait until the algorithm finishes. This will take some time for this large size! I tested this with the lipid PS2e and got an area per lipid of 64 in the end. 2.) As alternative, if you need a very dense packing, you could define a membrane size of eg. 750x750. Use "The Wanderer". Activate the "Wander for fellow" and the "Dance" option and increase the "Possible Missteps" size. Wait until the algorithm is finished. Then, you should have more lipids then 10,000 for each membrane side. Therefore, start the "Distributor" algorithm. Define here the number of lipids, just as mentioned in 1., and then click "Apply Counts". I did this on my 64 bit Laptop with 8 GB Ram. If you have further question, please just contact me directly. You can also send me your PDB file with the values which you need, and I generate the file for you. Best wishes, Björn Am 10.03.2014 15:21, schrieb RICHARD WOOD rwoodphd_+_msn.com: > Does anybody know of a reliable tool to build a cell membrane that is > larger than say 100 by 100 lipids per leaf? I've tried the CHARMM gui > and CELLmicrocosmos MembraneEditor, but neither work for my purpose. > I can build something that has 300 or 400 lipids per leaf, but I'd > like something larger than that (if possible). Who knows, something > as big as I want may not have been done before. > > TIA, > Richard > > --Boundary_(ID_q07+Rfl24XdTA/UnOl8mEQ) Content-type: text/html; CHARSET=US-ASCII Content-transfer-encoding: 7BIT

Richard,

the MembraneEditor is able to handle also larger membranes, but make sure that 1) you use a 64 bit machine and 2) you use a 64 bit Java version. With 32 bit you are completely right: this will not work.

If you are a user of Eclipse, you can also just download and import the project into your workspace from here:

http://cellmicrocosmos.org/index.php/download

In this case, do not forget to install Java 3D on your machine:

http://java3d.java.net

For your purpose, I would suggest two workflows:

1.) Easy: Define a membrane size of ca. 800x800, maybe a little bit larger. Use the Distributor algorithm. Type as Lipids EC 10,000 and Lipids IC 10,000 and press "Apply counts". Wait until the algorithm finishes. This will take some time for this large size! I tested this with the lipid PS2e and got an area per lipid of 64 in the end.

2.) As alternative, if you need a very dense packing, you could define a membrane size of eg. 750x750. Use "The Wanderer". Activate the "Wander for fellow" and the "Dance" option and increase the "Possible Missteps" size. Wait until the algorithm is finished. Then, you should have more lipids then 10,000 for each membrane side. Therefore, start the "Distributor" algorithm. Define here the number of lipids, just as mentioned in 1., and then click "Apply Counts".

I did this on my 64 bit Laptop with 8 GB Ram.

If you have further question, please just contact me directly. You can also send me your PDB file with the values which you need, and I generate the file for you.

Best wishes,
Björn

Am 10.03.2014 15:21, schrieb RICHARD WOOD rwoodphd_+_msn.com:

Does anybody know of a reliable tool to build a cell membrane that is larger than say 100 by 100 lipids per leaf? I've tried the CHARMM gui and CELLmicrocosmos MembraneEditor, but neither work for my purpose. I can build something that has 300 or 400 lipids per leaf, but I'd like something larger than that (if possible). Who knows, something as big as I want may not have been done before.

TIA,

Richard

--Boundary_(ID_q07+Rfl24XdTA/UnOl8mEQ)-- From owner-chemistry@ccl.net Tue Mar 11 09:12:00 2014 From: "Praveen Kumar pravink068.+*+.gmail.com" To: CCL Subject: CCL: velocity autocorrelation function calculation in gromacs Message-Id: <-49833-140311074439-21255-f5w63eZgEUoeVFL89I6Q4Q+*+server.ccl.net> X-Original-From: Praveen Kumar Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 11 Mar 2014 17:14:32 +0530 MIME-Version: 1.0 Sent to CCL by: Praveen Kumar [pravink068||gmail.com] Hi, I am trying to calculate vacf for ions by GROMACS 4.5.4. But I am not getting right value, if i am using residue.If i used whole molecule (not ion), i got right value for that. Can anybody help me to understand how to resolve this problem? I want to calculate vacf for ions. Thanks. PRAVEEN