AMBER Archive (2009)

Subject: Re: [AMBER] Atom type error

From: Vikas Sharma (vs_vikassharma_at_yahoo.co.in)
Date: Sun Apr 19 2009 - 13:33:36 CDT

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_at_biomaps.rutgers.edu>
To: AMBER Mailing List <amber_at_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

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