Hi,
The LCPO algorithm needs to know how many bonds each atom has to work
correctly. Unfortunately the current version of cpptraj is not able to
create bond information from PDB files; this feature will be present
in the next version of cpptraj, available in the upcoming release of
AmberTools 12.
Currently, as long as the PDB has the same # of atoms and residues as
the prmtop they can be used together. Something like:
parm prmtop.movie0.parm7
trajin movie0.pdb
should work fine. If you're having trouble creating a prmtop for your
PDB with leap maybe you could post 1 frame from the PDB file in
question so I and others can give some suggestions.
-Dan
On Thu, Mar 15, 2012 at 12:15 PM, Dmitry Osolodkin <divanych.rambler.ru> wrote:
> 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:
>
> BEGIN TRAJECTORY PROCESSING:
> ----- [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,
> Dmitry
>
>
> 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<divanych.rambler.ru> 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
>>> ENDMDL
>>> 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
> Researcher
> Group of Computational Molecular Design
> Department of Chemistry
> Moscow State University
> Moscow 119991 Russia
> e-mail: dmitry_o.qsar.chem.msu.ru
> Phone: +7-495-9393557
> Fax: +7-495-9390290
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 15 2012 - 10:00:02 PDT
