I still have the same proplem, even with TER (and it's just a simple peptide pdb file) but it works fine with tleap.
Houcemeddine
________________________________________.
From: Vishal Kumar Jaiswal [vishal3990.gmail.com]
Sent: Friday, June 29, 2012 1:30 PM
To: AMBER Mailing List
Subject: Re: [AMBER] no hydrogen added with xleap
if you have a pdb file check that you have TER between strands at proper
places.
maybe this can help
vishal
On Fri, Jun 29, 2012 at 1:25 PM, houcemeddine othman <
houcemeddine.othman.pasteur.rns.tn> wrote:
>
> Hi,
> I use xleap to build a PCA residue in my protein tail. When I try to load
> my molecule to xleap after assigning the force field parameters, I find
> that the program did not add the hydrogen atoms to the protein. This did
> not make any problem with tleap, where the hydrogens are properly added to
> the protein structure. I tried to use the edit graphical window and use
> the Add hydrogen & build optio in xleapn. The structure seems to have wrong
> valence assignment. Xleap seems to add the hydrogen atoms without
> considering the connection between the in the amino acid. in other word
> I've obtained an ensemble of atoms without any connectivity between them.
> Have you any idea about this problem?
>
> best regards
> Houcemeddine Othman
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>
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Received on Fri Jun 29 2012 - 05:30:02 PDT
