[gmx-users] missing atoms

David van der Spoel spoel at xray.bmc.uu.se
Tue Aug 1 16:06:17 CEST 2006

ninoo mani wrote:
> Dear gmx users
> I have a protein molecule with few missing residues,
> a Lys with CG, CD, CE, NZ missing atoms, and
> a Val with CG1, CG2 missing atoms.
> I noticed that pdb2gmx reads the pdb file and places the missing atoms.

Are you sure? I'm not aware of such a feature.

> First I want to know whether gromacs places only missing atoms or it 
> places the entire side chain?
> Second, is gromacs' repaired molecule reliable for simulation or I 
> should do homology modelling using other softwares to repair the molecule?
> Thanks,
> Ninoo
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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