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Dear Justin Thank you for your reply. this simulation contains a peptide and water in a specified pH. Do you think this .pdb file is correct. Thank you Kargar > > > Faezeh Kargar wrote: >> Dear All >> >> I asked this question in Martini's forum, but tile now no answer, so I >> had to ask it here. excuse me. >> I did an atomistic peptide simulation. TheĆ residues and positions of >> all atoms in this peptide created by my self, I mean I didn't download >> the pdb file from <www.pdb.org>. at the end of atomistic simulation I >> have .pdb and .gro files that show the minimized structure of the >> peptide. >> >> Now I have a question: Can I use the last pdb file for a CG peptide? Can >> I use atom2cg.awk and seq2itp.pl in this case? >> > > You can run those scripts on any syntactically-correct .pdb file. > > -Justin > >> Thank you >> Kargar >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- 83_kargar -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
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