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.
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 | (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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