Hi, I want to ask you for help. I've got a trr file after 5 ns simulation on the desktop 2 quad. The object is a complex of protein and ligand (the itp file for ligand was prepeared by server), in adition, I made some changes in rtp, atp, bon.itp databases to obtain a phosphorylated tyrosine. When I used a trjconv command to convert trr to xtc or to pdb I found that my comlex in the first frame was devided between several cells (the result of the standard command). So I tried different variants to gather everything in one cell:
1)trjconv -f sys1md.trr -s sys1md.tpr -o dyrk_ehb1.pdb -sep -n sys1em1.ndx -b 1 -e 100 -skip 10 -pbc nojump 2) trjconv -f sys1md.trr -s sys1md.tpr -o dyrk_ehb2.pdb -sep -n sys1em1.ndx -b 1 -e 100 -skip 10 -center -pbc mol -ur compact I've even tried to follow one variant by another. But the results are the same. As you see I can loose my ligand or phosphate from tyrosine. Index file, I used in the command, contains a new group "complex", which includes atoms of protein without hydrogenes, ligand with hydrogenes. I've got a one more result, but I can't find this file. In those case I loosed some other aminoacids, but ligand and phosphate are Ok. Thank you (P.S. I sent a letter with attached sample pdb files, but moderators didn't passed it) -- 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
