Hi there, Please, let me suggest to look at acpypi.googlecode.com. You may find at wikis some answers to your questions.
I hope it helps. Alan On Thu, Oct 1, 2009 at 02:34, <[email protected]> wrote: > Message: 2 > Date: Thu, 01 Oct 2009 09:17:02 +1000 > From: Mark Abraham <[email protected]> > Subject: Re: [gmx-users] good Atom type in gromacs with the AMBER ff > port > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > ABEL Stephane 175950 wrote: >> Hi gromacs users >> >> I have a newbie question about the atom type in gromacs. I would like to >> simulate a peptide with AMBER ff (ffamber03) in gromacs v.4.05 , so I have >> downloaded the ffamber files and followed the explanation given in Sorin's >> lab homepage. To neutralize my system i have added one CL- ion in the >> simulation box, but i am not sure it was good ion (in a other word the CL- >> ion compatible with the AMBER ff and not the default ion parameters). Here >> what i did > > Unfortunately at various points various strings have to match, and "CL-" > is different from "Cl-" from "CL" > >> - Added ions.itp file the following directive: >> >> #ifdef _FF_AMBER99 >> [ moleculetype ] >> ; molname nrexcl >> Cl- 1 > > This one needs to match the contents of your [ system ] directive. > >> [ atoms ] >> ; id at type res nr residu name at name cg nr charge mass >> 1 amber99_30 1 CL- CL 1 -1 >> 35.4530 > > The one on the left needs to match the residue name field of your > structure file, and the one on the right needs to match the name in the > atom name field of your structure file. (If you're using pdb2gmx, that > atom name field would need to match the name in the atom type database too!) > > I don't know which of these needs to match the name given on the genion > command line, but it'll be one of them. > > Mark > >> #endif >> >> - Use the following command with genion >> >> genion_mpi -s ions.tpr -o beta-I-Ac-NH2_slv_AMBER_ions.gro -p topol.top >> -pname NA+ -nname CL- -nn 1 -> genion passes correctly >> >> It is correct ? If not what is wrong ? >> >> Thanks in advance for your help. >> >> Stéphane > -- Alan Wilter Sousa da Silva, D.Sc. PDBe group, PiMS project http://www.pims-lims.org/ EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK +44 (0)1223 492 583 (office) _______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
