Message: 2 Date: Tue, 01 Aug 2006 16:06:17 +0200 From: David van der Spoel <[EMAIL PROTECTED]> Subject: Re: [gmx-users] missing atoms Hi Ninoo,
GROMACS will definitely give you warnings over missing atoms, but won't to the best of my knowledge replace them as David pointed out. Try downloading swiss PDB viewer (www.expasy.org/spdbv/), once you load up your structure it will prompt you re. the missing atoms. When you say missing atoms...I presume you mean missing side chain atoms...if you have missing alpha carbons in your structure then I suggest you need to start thinking about homology modelling! If you are lucky enough to have access to insightII in your lab, then you can use that package. You should check for bad contacts once you have put in your missing atoms, perhaps do a short cycle of steepest descent energy minimization with GROMACS!? Hope that helps cheers Kia To: Discussion list for GROMACS users <[email protected]> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=windows-1252; format=flowed 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 -- Kia Balali-Mood PhD, CBiol, MIBiol Postdoctoral Research Associate, Department of Biochemistry, Oxford University, OX1 3QU, UK sansom.biop.ox.ac.uk/kia/ , tel. +44 (0)1865 275 (380 or 275) _______________________________________________ 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
