Dear Mark Thank you for your important notes,I didn't know them.
Then,Can it be resulted from your sentences , there is not any way for doing simulation with only some parts of a protein? What can I do if I need simulating only ACTIVE SITE of a protein?Do I have to simulate the whole of protein? Thanks in advance On Tue, Apr 5, 2011 at 11:58 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 5/04/2011 5:09 PM, mohsen ramezanpour wrote: > >> Dear Mark >> >> Actually I don't know why. >> I just did the normal process as other my simulations. >> >> Let me discribe my work in details: >> I had a protein and a drug,I separated all residues around my drug (2 nm >> in radius) by PYMOL >> > > You can't do that and hope for sensible results. The protein won't be happy > if you expose its hydrophilic core to either a box of solvent or vacuum or > implicit solvent. > > > Then I saved the result as protein-new.pdb >> So.I used pdb2gmx to generate .top and .gro file for this .pdb file >> > > pdb2gmx assumes you're giving it reasonable input - i.e. no missing > residues in the protein. However, you've generated several chunks of missing > residues above. pdb2gmx assumes there's a backbone peptide bond as normal, > and this is too long. One can work around this issue, but still be crippled > by the first problem. > > > I entered the following commands for pdb2gmx: >> pdb2gmx -f protein-new.pdb -o protein-new.gro -p topology.top >> -water spc -ignh >> and I used Gromos 43a1 force field. >> >> when I want to do EM there are an additional error that results in >> crashing the mdrun: >> Warning: 1-4 interaction ... your system is exploding >> >> it says modifying interaction tables! >> >> Besides,I checked my pdb file,atoms 922 and 943 and 2 others who have bad >> interactions,all of them are N atom of residues! >> > > Yep, pdb2gmx has generated backbone peptide bonds that aren't sensible. > > > Mark > -- > 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 >
-- 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