Okay, I am trying AmberTools as well. Thanks Justin! Majid
________________________________ From: Justin A. Lemkul <[email protected]> To: Gromacs Users' List <[email protected]> Sent: Sun, April 10, 2011 10:16:57 AM Subject: Re: [gmx-users] Dangling bond error for dna majid hasan wrote: > Is there any software that generates .pdb file consistent with amber > forcefield >requirements? I tried 3DNA, and GABEDIT, but 3DNA doesn't name residues in >correct format i.e DX, and gabedit names every residue as DX3. > Perhaps xleap (part of AmberTools), but if your input has a bunch of incorrect atoms, I don't know how well it deals with replacing them. I seem to remember that it just writes new atoms and doesn't necessarily clean up the old ones, but my memory could be incorrect or the program may have been improved since last I tried it. http://ambermd.org/#AmberTools -Justin > Thanks, > Majid > > ------------------------------------------------------------------------ > *From:* Justin A. Lemkul <[email protected]> > *To:* Gromacs Users' List <[email protected]> > *Sent:* Sun, April 10, 2011 4:17:59 AM > *Subject:* Re: [gmx-users] Dangling bond error for dna > > > > majid hasan wrote: > > Sorry, the pdb file is bigger than 50k so it won't attach, so its pasted >below. Output of pdb2gmx is attached. > > > > You have numerous problems with this .pdb file: > > 1. All residues are listed as being the 3' end form. Your chain should start >with a 5' end, include the "middle" residues, and end with a 3' form. > > 2. 5' ends do not have phosphate on them, per force field convention. > > 3. You have various incorrect atoms, and some incorrect atom names. > > Please refer to the dna.rtp file for your chosen force field to understand > its >expectations. Then you will need to manually fix your .pdb file by renaming, >replacing, or removing whatever is in conflict. > > -Justin > > -- ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu<http://vt.edu> | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- gmx-users mailing list [email protected] ><mailto:[email protected]> > 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 [email protected] ><mailto:[email protected]>. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ======================================== 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 [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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