Re: [AMBER] PDB trajectory format

From: Dmitry Osolodkin <>
Date: Thu, 15 Mar 2012 20:15:21 +0400

Dear all,

I have tried cpptraj for this system and it worked fine, thank you for
the advice. In the same time, another problem has arisen: when trying to
calculate surface with surf command, it says:

----- [movie.0.pdb] (1-2001, 1) -----
     .... Setting up 1 actions for structure_initial.pdb ....
Error: SetSurfaceInfo(): Parm structure_initial.pdb does not contain
bond info.
       SURF: Setting up parameters for 17692 solute atoms.
             LCPO surface area will be calculated for 17692 atoms.

Does it mean that cpptraj's surf won't work with pdb trajectory taking
in mind that differences between the pdb file and prmtop file
constructed from it will be too crucial? When I try to construct prmtop
with xleap, it complains about split residues and creates atoms from
scratch. Are pdb trajectories compatible with prmtop topology in principle?

Thanks in advance,

On 03/03/2012 10:53 PM, Daniel Roe wrote:
> Hi,
> Have you tried cpptraj? It should be able to handle PDB files with
> multiple models correctly.
> -Dan
> On Sat, Mar 3, 2012 at 11:10 AM, Dmitry Osolodkin<> wrote:
>> Dear AMBER list,
>> I have a problem with externally generated PDB trajectory which I want
>> to analyse with ptraj. Namely, when I take it to ptraj using the first
>> frame as topology file, it says:
>> WARNING in checkCoordinates(): The actual number of atoms (35596304)
>> does not match the expected number of atoms (17692) in
>> (movie_filtered.pdb)
>> With this version of the code, this will likely lead to program
>> failure!!!
>> PTRAJ: rms first out CA.rms .CA
>> Mask [.CA] represents 1142 atoms
>> [No output trajectory specified (trajout)]
>> movie_filtered.pdb: 1 frames.
>> Obviously, ptraj interprets this trajectory as a single frame. The frame
>> delimiters are as follows (each frame consists of 4 chains delimited by
>> TER cards):
>> ATOM 17695 HG3 THR F1713 -1.488 -11.414 -19.211
>> TER
>> MODEL 2
>> ATOM 4 HN1 MET B 496 -32.564 32.599 -38.266
>> How should I modify the pdb trajectory to make it properly readable for
>> ptraj?

Dmitry Osolodkin, PhD
Group of Computational Molecular Design
Department of Chemistry
Moscow State University
Moscow 119991 Russia
Phone: +7-495-9393557
Fax: +7-495-9390290
AMBER mailing list
Received on Thu Mar 15 2012 - 09:30:02 PDT
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