Re: [AMBER] savePdb in leap

From: Jason Swails <>
Date: Fri, 5 Mar 2010 18:58:50 -0500


On Fri, Mar 5, 2010 at 8:47 AM, Peter Schmidtke
<> wrote:
> Dear Amber users/developers,
> I have a question related to leap (ambertools 1.2). When I prepare a system
> (solvation etc...) starting with a pdb structure and I dump the results to
> the topology & coordinate files (using saveAmberParm) and afterwards in the
> same session I dump the coordinates to a pdb file (savePdb), then the order
> of atoms in the pdb do not correspond to the order of atoms in the topology
> file written just before. Is this known, normal and corrected in
> ambertools1.3? Is it fixed by some new bugfix?

Are you using tleap or sleap? tleap occasionally has strange behavior
that doesn't affect results. For instance, run the following script
through tleap:

source leaprc.ff99SB

l = sequence {NALA ALA CALA}

k = copy l

saveamberparm l l.prm l.crd
saveamberparm k k.prm k.crd

If you then diff l.prm and k.prm, it will show you that a very large
part of the topology files are different. However, these prmtop files
will give identical MD/minimization results. Topology files work on a
pointer system, where some sections contain all of the parameters
while other sections contain 'pointers' that specify an atom/bond's
position in that list of parameters. Thus, a prmtop just has to be
consistent with regards to its sequence/parameters/pointers, and the
order is quite arbitrary. Long story short, it would not surprise me
if pdb files and prmtops created by tleap had differently-ordered
atoms (but maybe I'm mistaken).

As far as I know, the above script run through sleap creates identical
prmtops outside of maybe the time stamps.

> I did not try for now, but I saw a statement that ambertools1.3 writes pdb
> files using the new pdb standards. Does ptraj etc... write now the elements
> in the corresponding element columns or still not?
> Thanks in advance.

Did you try with the latest ptraj 1.3? I'm not sure exactly, as I
haven't been following PDB format specifications... Someone else
would have to comment more definitively on this.

Good luck!

> Peter Schmidtke
> ----------------------
> PhD Student at the Molecular Modeling and Bioinformatics Group
> Dep. Physical Chemistry
> Faculty of Pharmacy
> University of Barcelona
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Fri Mar 05 2010 - 16:00:02 PST
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