Thankyou. I was able to get .gro file. How can I specify a octahedron box for solvation. I am unable to get the syntax of the command right with -box and -bt. Jaya
On Fri, Sep 11, 2009 at 10:52 AM, Justin A. Lemkul <[email protected]> wrote: > > > jayalakshmi sridhar wrote: > >> Dear Gromacs users, >> I have a homology model of a protein. Te N-terminal is an ASP residue. >> When I run the command >> pdb2gmx -f protein.pdb -o protein.gro -ff G43a1 -p protein.top -i >> posre.itp >> I get the following error- >> Atom HA in residue ASP 1 not found in rtp entry with 9 atoms >> while sorting atoms. Maybe different protonation state. >> Remove this hydrogen or choose a different protonation state. >> Option -ignh will ignore all hydrogens in the input. >> The protein looks alright in Sybyl. How to get this working? Thanks for >> the help. >> > > G43a1 is a united-atom force field. Alpha-carbons are not explicitly > represented. So if you pass this structure to pdb2gmx, the program assumes > you have only the necessary atoms present. If you have unnecessary > hydrogens, use -ignh. > > -Justin > > Jaya >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://lists.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 >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > 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 [email protected] > http://lists.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 >
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