AMBER Archive (2004)

Subject: Re: AMBER: peoblemwith RED II

From: FyD (fyd_at_u-picardie.fr)
Date: Fri Aug 27 2004 - 05:02:37 CDT

Hi,

> Thanks for the reply. I was able to rectify the problem
> without modification to the RED source code. I have calculated the RESP
> charges and then created the frcmod and prepin files for the new residue.
> But now I face another problem.

OK

> 1. I made the modifications to the protein structure by attaching an
> organic molecule to an aminoacid residue in INSIGHT II. In the saved pdb
> file the attached organic molecule is present in the end of the file as
> the last residue. Now I load my prepin and frcmod files followed by this
> molecule in leap and make proper bonds between the organic molecule and
> the aminoacid. Now when I check this structure it shows a few warnings of
> close contacts and an error:

If I understand you, you have two part in your residue... The aminoacids and the
org. fragment.
This means you have two residues and you have a branched molecule...

> Created a new atom named: OXT within residue: .R<ALA 582>

Did you check the atom names of this ALA 582? It must match the ones in the ALA
OFF library of xleap.

> How to overcome this problem?

Check carefully the atom name AND residue name in your PDB file and in your
xleap OFF libraries...
They have to be the same...

> 2. Next I tried to make modifications at 2 aminoacids. Now when I tried to
> load this structurte in leap, leap aborts with this error:
>
> ERROR: Comparing atoms C15, H161, H162, H163 to atoms C15, O11, H161, H162
> !FATAL ERROR----------------------------------------
> !FATAL: In file [chirality.c], line 120 !FATAL: Message: Atom O11 is not
> in the first list
> !ABORTING.

First see http://amber.scripps.edu/bugfixes/8.0/bugfix.15

I wonder if your problem does not come from the fact that your have two residues
in this new aminoacid and consequently that you have a brached molecule.
I had this problem once and was able to solve it checking carefully the 'head'
and 'tail' of each residue...
See the xleap documentation for this.
Moreover, I wonder if you should not had a TER character between the two parts
of your new aminoacids in your PDB file as your molecule is branched...

Regards, Francois
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