[gmx-users] good Atom type in gromacs with the AMBER ff port

ABEL Stephane 175950 Stephane.ABEL at cea.fr
Thu Oct 1 01:04:06 CEST 2009

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

- 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. 


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