[gmx-users] How to correct incomplete pdb file
lindahl at sbc.su.se
Thu Nov 17 23:12:03 CET 2005
Modeller is quite powerful when building general homology models, but
might be a bit of overkill just to fix a sidechain. You can try a
simple frozen approximation and just scan for individual rotamers -
we have a very naive web implementation (screws up chain identifiers
right now) at
On Nov 17, 2005, at 6:12 PM, Nathan C. Rockwell wrote:
> You might try Modeller, available from the Sali lab web site
> (salilab.org, I think, but easiest to just google it). Other
> options have recently been compared in Protein Science 14:1315-27.
> On 11/16/05 7:20 PM, "Hiromichi Tsurui" <tsurui at med.juntendo.ac.jp>
>> Thank you, Tsjerk;
>> I would like to try. But I have never used a kind of modeler soft.
>> Does SwissPDB voewer works as a modeler soft ? Is it possible to
>> save corrected pdb file using SwissPDB viewer ? If not, what
>> software is available ?
>> Many Thanks.
>>> ----- Original Message -----
>>> From: Tsjerk Wassenaar <mailto:tsjerkw at gmail.com>
>>> To: Discussion list for GROMACS users <mailto:gmx-users at gromacs.org>
>>> Sent: Thursday, November 17, 2005 6:00 AM
>>> Subject: Re: [gmx-users] How to correct incomplete pdb file
>>> Hi Hiromichi,
>>> You have to add missing side chains using a modeler. When you
>>> load the protein in SwissPDB Viewer, this will automatically be
>>> done. Be sure to also check the protein for missing residues.
>>> This should be indicated in the PDB file. The option -ignh is of
>>> no use at all in this case.
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Erik Lindahl <lindahl at sbc.su.se>
Assistant Professor, Stockholm Bioinformatics Center
Stockholm University, SE 106 91 Stockholm
Phone: +46 8 5537 8564 Fax: +46 8 5537 8214
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