Ok ! Thank you everybody for your help
Stephane
Message: 3
Date: Wed, 30 Sep 2009 19:36:26 -0400
From: "Justin A. Lemkul" <[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
- Added ions.itp file the following directive:
#ifdef _FF_AMBER99 [ moleculetype ] ; molname nrexcl Cl- 1
[ atoms ] ; id at type res nr residu name at name cg nr
charge mass 1 amber99_30 1 CL- CL 1
-1 35.4530 #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 ?
Why wouldn't it be? There's only one entry for Cl- in ffamber03.atp. Makes the
choice fairly easy :)
-Justin
Thanks in advance for your help.
Stéphane _______________________________________________ gmx-users mailing
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