Re: [AMBER] Problem related to Missing amino acids in pdb

From: David A Case <case.biomaps.rutgers.edu>
Date: Wed, 15 Jun 2011 08:27:37 -0400

On Wed, Jun 15, 2011, Sindrila Dutta banik wrote:
>
>
> I have a crystal structure of an enzyme (HisRS) which is tetramer. The
> residues between 185 to 228 are missing for all chains. How to manage
> this issue?
>
>
> Now I want to make the carboxylic acid group (-COO-) of 185 residue and
> amino group of (-NH3+) residue 228 as neutral. How to do this? I also
> want to know in general what is used in such cases.

Just to repeat recent advice on a similar problem:

One solution is to edit the leaprc file you are using (keeping a
backup copy of course), changing the AddPdbResMap part (this is the part
that tells LEaP to convert N- and C-terminal residues to their charged
counterparts).

The above is a bit of a guess: it allows control over which terminal
substitutions are made, and so may serve your needs.

...dac


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Received on Wed Jun 15 2011 - 05:30:04 PDT
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