Thanks! Problem solved!!! ________________________________________ From: [email protected] [[email protected]] on behalf of Justin Lemkul [[email protected]] Sent: Saturday, October 13, 2012 10:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] error: group protein not found in index file
On 10/13/12 10:32 PM, Liu, Hanzhong wrote: > Hi All: > I'm trying to set up a small box with only water and ions (no protein) > and run MD simulation. The commands I used to set up my system and running MD > are as follows: > > genbox -cs spc216.gro -o water.gro -maxsol 256 -box 2.1 2.1 2.1 > pdb2gmx -f water.gro -q water.pdb -n index.ndx > grompp -f ions.mdp -c water.gro -p topol.top -o ions.tpr > genion -s ions.tpr -o water_ions.gro -pname NA -nname CL -nn 23 -np 23 > -rmin 0.44 -p topol.top > grompp -f mini.mdp -c water_ions.gro -p topol.top -o em.tpr > mdrun -v -deffnm em > grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr > > And then I received the error message > > Fatal error: > Group Protein not found in index file. > Group names must match either [moleculetype] names > or custom index group names,in which case you > must supply an index file to the '-n' option of grompp. > > Then I tried using make_ndx -f water_ions.mdp -o index.ndx to generate index > file and tried grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr - > index.ndx but still didn't work. In my system, there is no protein, so how > can I setup the system correctly and run MD. Thanks! > If there is no protein, don't specify "Protein" anywhere in your .mdp file. Likely this is one of your tc-grps. You should probably be using "System" for this setting. -Justin > -------------------------------------------------------------------------------------------- > what's in top file: > > [ system ] > ; Name > Generated by genbox > > [ molecules ] > ; Compound #mols > SOL 210 > NA 23 > CL 23 > -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
