Dear users, Firstly thanks for your replies. I have two ligands as I said before. I will analyze the system together ligands after the simulation is finished. For example: I want to plot potential energy of all system (that is, protein+LİGA+LİGB) by g_energy. Then, Should I create the groups as the following?
*energygrps = Protein LİGA_LİGB* tc-grps = Protein_LİGA_LİGB Water_and_ions OR *energygrps = Protein LİGA LİGB* tc-grps = Protein_LİGA_LİGB Water_and_ions Thanks 12 Mayıs 2011 18:29 tarihinde lina <[email protected]> yazdı: > 2011/5/12 Justin A. Lemkul <[email protected]>: > > > > > > lina wrote: > >> > >> make_ndx -f your.gro/pdb -n your.ndx -o your.ndx > >> > >> LiGA & LİGB: > > > > This is not correct. You need to use | rather than &. Using logical and > > (&) means the index group will contain atoms that are common to both LIGA > > and LIGB. If they are distinct entities, the group will be empty. > Logical > > or (|) says merge the two different groups to create one unified group. > > Ooops > > > > > > -Justin > > > >> q > >> > >> in grompp add -n your.ndx > >> > >> > >> 2011/5/12 ahmet yıldırım <[email protected]>: > >>> > >>> Dear users, > >>> > >>> I have two ligands. I created a special index group that merges the > >>> protein, > >>> LiGA and LİGB. > >>> > >>> I have the pr.mdp file as the following: > >>> ... > >>> energygrps = Protein LİGA_LİGB > >>> tc-grps = Protein_LİGA_LİGB Water_and_ions > >>> ... > >>> > >>> grompp -f pr.mdp -p topol.top -c em.gro -n index.ndx -o pr.tpr > >>> Fatal error: > >>> Group LİGA_LİGB not found in indexfile. > >>> > >>> I get the fatal error since I dont have a special index group that > merges > >>> LiGA and LİGB. should I create two different index file? > >>> > >>> Thanks in advance > >>> -- > >>> Ahmet YILDIRIM > >>> > >>> -- > >>> 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 > >>> > >> > >> > >> > > > > -- > > ======================================== > > > > Justin A. Lemkul > > Ph.D. Candidate > > ICTAS Doctoral Scholar > > MILES-IGERT Trainee > > 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 > > > > > > -- > Best Regards, > > lina > -- > 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 > -- Ahmet YILDIRIM
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