I have solved this problem by all your advices. Thank you, Mark and Yang Ye for your help!
>That wasn't the advice Yang Ye gave you... see >http://www.gromacs.org/pipermail/gmx-users/2007-February/025792.html > >For a simpler solution, see >http://www.gromacs.org/pipermail/gmx-users/2007-February/025796.html > >Mark >Message: 6 >Date: Wed, 07 Feb 2007 22:29:36 +0800 >From: Yang Ye <[EMAIL PROTECTED]> >Subject: Re: [gmx-users] Error:4 atoms are not part of any of the > T-Coupling groups >To: Discussion list for GROMACS users <[email protected]> >Message-ID: <[EMAIL PROTECTED]> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > >Interesting that you have your Ca2+ ions in the beginning of your >structure file. In this case, remove the line [ SOL ] and replace [ CA ] >with [ SOL ]. >Although, changing your mdp file to have "Protein Non-Protein" is simpler. > >The rationale behind is that the *groups* included for the tc-grps shall >cover all atoms. > >On 2/7/2007 9:34 PM, Qiang Zhong wrote: >> Hollow: >> I have post my question last time,my emailbox can not work, So I post >> again. >> I have 4 calcium ions bind at protein, when I use command: >> grompp -f fullmd_sol.mdp -c minimized_water.gro -p cln.top -o fullmd.tpr >> >> I got error message: >> Fatal error: >> 4 atoms are not part of any of the T-Coupling groups >> >> I got a advice to use : >> make_ndx -f minimized_water.gro >> >> Then I got a file index.ndx >> I find the line in index.ndx ,just like below: >> 57378 57379 57380 57381 >> [ CA ] >> 1 2 3 4 >> [ SOL ] >> Then I delete them,and run again: >> grompp -n index.ndx -f fullmd_sol.mdp -c minimized_water.gro -p cln.top -o >> fullmd.tpr >> >> But Error still there. >> >> Could somebody tell me how to do? >> Thank you very much! _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
