But in coordinate file(.pdb file) ,I am not getting the atoms which belongs to DPPC.only I have included the name of dppc.itp file like this: ;Include DPPC chain topology #include "dppc.itp"
That's why I have found the atoms wich belongs to DPPC molecule from dppc.itp file itself. On Wed, Feb 1, 2012 at 12:40 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 1/02/2012 6:04 PM, Anushree Tripathi wrote: > > When I run the command (i.e., make_ndx -f em.gro -o index.ndx) ,it is > showing the following options: > 0 System : 18379 atoms > 1 Protein : 11739 atoms > 2 Protein-H : 9135 atoms > 3 C-alpha : 1173 atoms > 4 Backbone : 3519 atoms > 5 MainChain : 4693 atoms > 6 MainChain+Cb : 5773 atoms > 7 MainChain+H : 5842 atoms > 8 SideChain : 5897 atoms > 9 SideChain-H : 4442 atoms > 10 Prot-Masses : 11739 atoms > 11 non-Protein : 6640 atoms > 12 Water : 6636 atoms > 13 SOL : 6636 atoms > 14 non-Water : 11743 atoms > 15 Ion : 4 atoms > 16 CL : 4 atoms > 17 Water_and_ions : 6640 atoms > > > So your system has 18K atoms, with 11K protein and the rest solvent and > ions. As Justin suggested, this coordinate file does not have DPPC in it. > > > > for my work, I used 16|13 then 1|11.lastly I saved it using 'q'.But there > is no option for DPPC (as given in tutorial we have to merge protein with > DPPC).After runing the command (grompp -f nvt.mdp -c em.gro -p topol.top -n > index.ndx -o nvt.tpr),it is showing error: > > Group DPPC not found in indexfile. > Maybe you have non-default goups in your mdp file, while not using the > '-n' option of grompp. > In that case use the '-n' option. > > To troubleshoot the error,I have kept one more group in index.ndx file > with number of atoms which I found from dppc.itp file(at the end of file) > like this > > [DPPC] > 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 > 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 > 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 > 46 47 48 49 50 > > > These numbers have to reference the atom numbers in the coordinate file, > not the [moleculetype]. Since you've done the latter, you get the problem > with T-coupling groups. But go back and use a coordinate file that actually > has DPPC in it. > > Mark > > > > Again after running the grompp command (grompp -f nvt.mdp -c em.gro -p > topol.top -n index.ndx -o nvt.tpr),I am getting the following error: > > Atom 1 in multiple T-Coupling groups (1 and 2). > > Please suggest me the reason as well as solution for this problem. > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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