Re: [AMBER] disulfide bridge -reg

From: Jeyaram R A <>
Date: Tue, 6 Mar 2018 05:56:51 +0000

Thank you very much sir, I follow your second suggestion i.e. pdb4amber, now i can able to connect the disulfide bridge in the protein.
                                                          Thank You
From: David A Case <>
Sent: Monday, March 5, 2018 6:30 PM
To: AMBER Mailing List
Subject: Re: [AMBER] disulfide bridge -reg

On Mon, Mar 05, 2018, Jeyaram R A wrote:
> > bond bnm.27.SG bnm.126.SG
> bond: Argument #1 is type String must be of type: [atom]

You can use the "desc" command in tleap to interrogate your system. For

   desc bnm.27

will show you the residue names and atoms in residue 27. It could be
that the residue numbers have been changed from what you expect, or
something else could be going on.

To expand on another reply email: it is indeed a good idea to use
pdb4amber first. Among other things, it will create CONECT records in
the output pdb file (look for them at the bottom of the file), which
tleap can use to create the proper disulfide bonds.

...good luck...dac

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