Re: [AMBER] Atom type error

From: Vikas Sharma <vs_vikassharma.yahoo.co.in>
Date: Sun, 19 Apr 2009 19:33:36 +0100

Dear Dr. David Case Thanks a lot for the mail..before getting your reply i tried that and got going Now after loading the protein i wanted to solvate it, so i found out the charge in xleap using 'charge ' command..it comes out to be : 'total perturbed charge = 9.000100 'total unperturbed charge = 9.000100' i added 9 Cl- bt the charge still remains 0.000100... what should i do now... Thanks a lot ________________________________ From: David A. Case <case.biomaps.rutgers.edu> To: AMBER Mailing List <amber.ambermd.org> Sent: Sunday, 19 April, 2009 11:11:11 PM Subject: Re: [AMBER] Atom type error On Sun, Apr 19, 2009, Vikas Sharma wrote: > Thanks for the reply..but its the problem with the protein...since > i prepared the protein in sybyl it has deprotonated the -COOh and > protonated the -NH2. This is the default for Amber as well.  It could be that the residue names for the N- and C-terminal residues are not Amber's (or the atom names).  Should be simple to just edit the PDB file to make things match. > >  Fatal: Atom .R<CXL 232>.A<C 1> doesnt have a type > >  Fatal: Atom .R<CXL 232>.A<O2 2> doesnt have a type > >  Fatal: Atom .R<CXL 232>.A<O1 3> doesnt have a type > >  Fatal: Atom .R<AMN 233>.A<N 1> doesnt have a type Amber doesn't know anything about residues named "CXL" or "AMN" -- you will need to edit the PDB file to be more standard. The usual rule of thumb applies here: you have to keep editing your PDB file until LEaP stops complaining.... ...dac _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber Connect with friends all over the world. Get Yahoo! India Messenger at http://in.messenger.yahoo.com/?wm=n/
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Received on Wed May 20 2009 - 11:46:06 PDT
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