[gmx-users] Adding hydrogen

Hi all users, Is it possible to add hydrogens to some of the selected atoms in the system using pdb2gmx? With best regards, Naser -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please sear

RE: [gmx-users] pdb file for ammonia

It is easy to make one yourself. I would use molden to draw ammonia and save as pdb file. You might need to minimize before using for md. Abu > Date: Thu, 31 Dec 2009 16:21:29 -0500 > From: nishap.pa...@utoronto.ca > To: gmx-users@gromacs.org > Subject: [gmx-users] pdb file for amm

RE: [gmx-users] topolbuild1_2_1.tgz decompressing problem

I had the similar problem but I untar it in two step to get around it: 1st gunzip *.tgz 2nd tar it in usual without z option > Date: Mon, 17 Aug 2009 08:25:15 +0200 > From: sp...@xray.bmc.uu.se > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] topolbuild1_2_1.tgz decompressing

RE: [gmx-users] no ngmx?

Hi Barbara, Possibly header files of x-windows not in the path and therefore, ngmx was not compiled during compilation. Abu > Date: Mon, 16 Mar 2009 17:46:06 +0100 > From: gioffr...@uni-duesseldorf.de > To: gmx-users@gromacs.org > Subject: [gmx-users] no ngmx? > > Hello

[gmx-users] Abu added you as a friend on Reunion.com!

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RE: [gmx-users] spliting clusters.pdb

Hi Jochen, Thanks for your replay. I manage to do that using trjconv. However, I will keep your suggestion in my mind for future use. > Date: Wed, 22 Oct 2008 18:04:01 +0200> From: [EMAIL PROTECTED]> To: > gmx-users@gromacs.org> Subject: Re: [gmx-users] spliting clus

[gmx-users] spliting clusters.pdb

Hi All, I have been wondering whether there is any tools for spliting clusters.pdb file into individual snapshots. With regards, Abu _ Win an Xbox 360 or £200 Top Shop Vouchers http://clk.atdmt.com/GBL/go/115454062/dir

RE: [gmx-users] compilation problem with mopac in gromacs 3.3.3

; To: gmx-users@gromacs.org > Subject: [gmx-users] compilation problem with mopac in gromacs 3.3.3, and > x86_64 machine > > >> Message: 1 >> Date: Tue, 8 Jul 2008 10:18:30 + >> From: Abu Naser >> Subject: [gmx-users] compilation problem with mopac in groma

RE: [gmx-users] compilation problem with mopac in gromacs 3.3.3, and x86_64 machine

s 3.3.3, and > x86_64 machine > > > > Message: 1 > > Date: Tue, 8 Jul 2008 10:18:30 + > > From: Abu Naser <[EMAIL PROTECTED]> > > Subject: [gmx-users] compilation problem with mopac in gromacs 3.3.3 > > and x86_64 machine > >

[gmx-users] compilation problem with mopac in gromacs 3.3.3 and x86_64 machine

Hi Gerrit, I am having problem during compilation as : /mdlib/.libs/libmd_d.a(qm_mopac.o): In function `call_mopac_SH': qm_mopac.c:(.text+0x2fc): undefined reference to `domop_' ../mdlib/.libs/libmd_d.a(qm_mopac.o): In function `call_mopac': qm_mopac.c:(.text+0x831): undefined reference to `dom

[gmx-users] keeping 4 atoms on a plane fixed during md run

Hi All User, Is there any way I can fix 4 atoms in a plane during MD run? Advice much appreciated, Abu _ All new Live Search at Live.com http://clk.atdmt.com/UKM/go/msnnkmgl001006ukm/direct/01/

[gmx-users] AFMM parameter refinement

Hi All, Has any body tried doing parameter refinement using Vaiana's python code called afmm.py? A.C. Vaiana, Z. Cournia, I.B. Costescu and J.C. Smith, "AFMM: A molecular mechanics force field vibrational parametrization program'", Computer Physics Communications, 167 (2005), pp.34-42. I hav

RE: [gmx-users] Avoiding parameterization step

Hi Gerrit, Thank you very much for your response. I am at the moment interested in doing conformational search. Is there any good paper that explain nicely about doing the charge distribution calculation? With regards, Abu > Date: Tue, 11

[gmx-users] Avoiding parameterization step

Hi All User, I have been wondering whether it is advisable to avoid parametrization step by freezing the atoms in MD simulation. With regards, Abu _ Free games, great prizes - get gaming at Gamesbox. http://www.searchg

[gmx-users] Avoiding parameterization step

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[gmx-users] Avoiding parameterization step

Hi All User, I have been wondering whether it is advisable to avoid parametrization step by freezing the atoms in MD simulation. With regards, Abu _ Share what Santa brought you https://www.mycooluncool.com_

[gmx-users] Avoiding parameterization step

Hi All User, I have been wondering whether it is advisable to avoid parametrization step by freezing the atoms in MD simulation. With regards, Abu _ Who's friends with who and co-starred in what? http://www.searchgamesb