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 ? Thanks in advance for your help. Stéphane _______________________________________________ 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
