Quoting Liu Shiyong <[EMAIL PROTECTED]>: > Hi, Mark, > Thanks for reply. > > > On Sun, Mar 9, 2008 at 1:41 AM, Mark Abraham <[EMAIL PROTECTED]> > wrote: > > > Liu Shiyong wrote: > > > Hi, all > > > > > > My purpose is to get the binding energy by gromacs. > > > > You can't do this without water. The binding energy involves displacing > > water interactions. > > > > Yes, But I just tried to get the binding energy by minimizing > protein-protein decoy without water. > > > > > > > > I tried to minimize protein-protein docking decoy by using gromacs > > > without water. But after being minimized, the ligand ran away from > > > receptor. > > > > "ran away" during what calculation? > > > > During minimizing ... > The following is my script. r-l_1.pdb is a protein-protein decoy structure. > > pdb2gmx -ff oplsaa -f r-l_1.pdb -p r-l_1.top -o r-l_1.gro -missing > > output.pdb2gmx 2>&1 & > grompp -f em.mdp -c r-l_1.gro -p r-l_1.top -o input.tpr > output.grompp 2>&1 > & > mdrun -nice 0 -v -s input.tpr -o minim_traj.trr -c minimized.gro -e > minim_ener.edr > output.mdrun 2>&1 & > > > > > > That's not what I expected . I just want to relax the protein-protein > > > interface due to some atom-atom contact crash . > > > > That's what position-restrained EM or MD is for. > > > > Yes, I will try position-restrained EM. Thanks for suggestion. > > > > > By the way, I found the net charge is not zero after adding H atoms on > > > complex by pdb2gmx. Can I solve the non-zero net charge problem by > > > adding H atom on receptor and ligand > > > > > > separately? > > > > Depends what's causing the non-zero charge. Integral non-zero charge is > > different from non-integral. Some integral charges are sensible, some > > aren't. > > > > The method of adding H atom that I used is > pdb2gmx -ff oplsaa -f r-l_1.pdb -p r-l_1.top -o r-l_1.gro -missing > > output.pdb2gmx 2>&1 & > It added all H atom on receptor and ligand at the same time. Is it a > possible reason for Integral non-zero charge ? > I want to try to add H atom on receptor and ligand , separately. > > Do you know how to add H atom on receptor and ligand , separately , and > combine them into one input file as minimizing ?
Separate your .pdb file into two - each protein in a separate file. Run pdb2gmx on each of these .pdb files, and include the output topologies as .itp files in your system topol.top, i.e.: protein_A.top --> protein_A.itp protein_B.top --> protein_B.itp #include both in your topol.top Doing this will allow you to see the net charge on each protein. Using the -missing flag with pdb2gmx is dangerous (as noted in the documentation). Is there a reason you're using this option? If atoms are missing from your model, that could be a source of some of the net charge you're seeing. If your charge is indeed integral, then it is likely due to the fact that many proteins bear some net charge; most are not perfectly balanced between positives and negatives! -Justin > > If I was wrong, please point out my mistake. Thanks. > > > > > > > Mark > > _______________________________________________ > > gmx-users mailing list [email protected] > > 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 > > > > > > -- > Shiyong Liu > Research Assistant > center for bioinformatics in the university of kansas > Lab: (785)864-1962 > Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED]) > Homepage: http://www.people.ku.edu/~syliu > Lab: http://vakser.bioinformatics.ku.edu/people > Phone: (785) 864-1962 > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] 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
