AMBER Archive (2009)

Subject: Re: [AMBER] creating new residue adds none wanted ter

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Mon May 04 2009 - 13:27:58 CDT

On Mon, May 04, 2009, Jorgen Simonsen wrote:
>
> TM = loadpdb nw_prot.pdb
>
> where I have changed the MET to MEM if I then
> savepdb TM rs_prot.pdb
>
> I can see in the pdb that it has added the TER to the new residue even
> though it is within a given sequence.

1. Look at rs_prot.pdb around the given residue. Is there any changes (e.g. a
change in chainID) that could trigger a new molecule?

2. Save a prmtop file, then use ambdpb to make the pdb file. Is the TER card
still there?

3. Look at the bonds, either in xleap, or in VMD by loading the prmtop file
first. Is there a bond between MEM and the next/precedding residue?

...good luck...dac

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