AMBER Archive (2008)

Subject: Re: AMBER: TERs

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Mon Feb 18 2008 - 11:18:36 CST

> 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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