Hi Mahnam, Thanks for your mail. Sorry, I do not get you whether you are talking on charge based on individual residue or on whole protein. As for as I know, autodock is not allowing non integer charge on residue basis and which implies that whole protein can also, should not have non integer as net formal charge and zero is not mandatory.
Please reply me. B.Nataraj On Wed, 29 Nov 2006 19:16:52 +0330, "Mahnam" <[EMAIL PROTECTED]> said: > In God We Trust > Hello Dear raja > I think that the charges in itp of Gromacs don't match with charges in > Autodock.Becase the total charge in Autodock is zero ,but the total > charges in itp of Gromacs are not zero ,then you can't use gromacs charge > for Autodock. > > Sincerely yours > Karim Mahnam > Institute of Biochemistry and Biophysics (IBB) > Tehran University > P.O.box 13145-1384 > Tehran > Iran > http://www.ibb.ut.ac.ir/ > > > > -----Original Message----- > From: Mark Abraham <[EMAIL PROTECTED]> > To: Discussion list for GROMACS users <[email protected]> > Date: Tue, 28 Nov 2006 12:47:14 +1100 > Subject: Re: [gmx-users] Script for coverting ITP and gro file to > Autodock > pdbqs > > > raja wrote: > > > Hi gmxions, > > > I want to use charge information contained in itp file produced in > > > gromacs for docking purpose (Autodock). Kindly share a script if > > anyone > > > written to convert information content from gromacs protein's itp > > (for > > > charge) and gro (coordinate) information to autodock pdbqs or pdbq > > > formated one. > > > > This sounds like a good exercise for learning how to use Perl. Get the > > file format descriptions and read a few chapters of a Perl reference. > > > > Mark > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > 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 > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A fast, anti-spam email service. _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
