Hi, On Wednesday, 5. September 2007 14:14, andrea carotti wrote: > Hi all, > I've performed my MD simulations using the charmm FF and NAMD (so > pdb,psf and dcd files). Now i would like to use the great GMX analysis > tools. I've successfully converted the dcd file in trr (using catDCD). > Now the next step I'd like to do is the psf to top conversion. I've seen > on the vmd site that a top2psf script is present but it not do the > reverse conv that i need. I would prefer to not pass through pdbs.I > would like to do this to not loose corrispondences of atoms and to not > miss parameters for not typical residues that I'm using (like > phosphrilated serines). > Is there someone that could help me on this topic?
Easiest solution (also fastest): Convert your files to multiple pdb, change residue names of HIS HIP (if they are not standard) than: dump first frame of this file as a reference pdb file convert the multiple pdb file to an xtc file trjconv -f your_multiple_pdb_from_namd.pdb -f your_multiple_pdb_from_namd.pdb -dump 0 -o 0.pdb trjconv -s 0.pdb -f your_multiple_pdb_from_namd.pdb -o protein.xtc Than you can run at least g_covar and show things, g_dist for example only works if you got an valid .tpr file. > Thanks in advance > Andrea > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php Greetings, Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
