AMBER Archive (2009)

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

From: Jorgen Simonsen (
Date: Tue May 05 2009 - 04:57:29 CDT


1. The residues look fine around the residue so I don't that causes the

2. I am not able to generate prmtop where I get the following error message
FATAL: Atom .R<ILE 277>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 303>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 314>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 328>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 334>.A<CD 20> does not have a type.

if I save the the structure

savepdb FR test.pdb

it add a CD with coordinates similar to CD1 getting one CD too much - the
strange thing is that it has five preceding residues correctly...

Any help appreciated
thanks in advance


On Mon, May 4, 2009 at 8:27 PM, David A. Case <>wrote:

> 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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