AMBER Archive (2008)

Subject: RE: AMBER: TERs

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Mon Feb 18 2008 - 11:51:51 CST

Hi Tom
I am using AMBER 8 and so I guess I like the ability to write TER cards
into the pdb files using ptraj (trajectory files to pdb).
I did run rdparm and it does separate the protein trimer incorrectly
which explains the restart files. I went back and looked at my original
pdb file used to generate the topology file and the "TER" lines are
correctly placed in that file with "OXT" atom types present at
C-terminus. So, I am not sure what happened.
It is really not a big problem since I can run analysis in ptraj without
correctly placed "TER" cards and I can easily add "TER" to the pdb files
once made.

Thanks, Steve

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of Thomas Cheatham
Sent: Monday, February 18, 2008 12:19 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: TERs

> I am having a problem with the pdb "TER" commands when I make pdb
files
> in amber. I have a three chain protein separated by "TER" in my
original
> pdb file. However, when I use ptraj to make pdb files from my
> trajectories, the print out of the pdb file has no TER lines and hence

Early versions of ptraj did not add TER cards; more recent versions do
add
TER card at molecule boundaries... This includes ptraj with AMBER9 and
more recent.

What version of ptraj?

> does not separate the chains. If I use ptraj to make "restart" files
> then use "ambpdb" to make my pdb files, the print out does have TERs
but
> in the incorrect locations. Any suggestions on what the problem is?

Make sure there is a complete match between the prmtop/restrt. Also,
you
can look at the molecule information with rdparm to understand where the

molecules are to make sure they are where you think they are...

rdparm prmtop
modifymol

-- tec3
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