Re: [AMBER] PDB trajectory format

From: Dmitry Osolodkin <divanych.rambler.ru>
Date: Fri, 16 Mar 2012 20:11:26 +0400

It seems reordering worked only for two shorter chains (my protein
contains two chains of 495 resides each and two of about 70 residues
each); atommap.dat attached.

My issues are not only with hydrogen atoms, but with all atoms:

Warning: reordered.structure_initial_copy_fix.pdb: Atom 17275 name [CA
] does not match parm name [H ]


On 03/16/2012 07:43 PM, Daniel Roe wrote:
> Hi,
>
> On Fri, Mar 16, 2012 at 11:08 AM, Dmitry Osolodkin<divanych.rambler.ru> wrote:
>> Warning: structure_initial_copy_fix.pdb: Atom 17081 name [HD22] does not
>> match parm name [HD23]
>>
>> The reason is obvious, but is this issue crucial for the LCPO algorithm?
>
> The LCPO algorithm only makes use of non-hydrogen atoms, so as long as
> your issues are only with hydrogens everything should be OK. The
> important thing is that the heavy atom ordering is the same so that
> the coordinates in the input PDB line up with what the topology file
> expects. For example, if in your topology your first residue is
> ordered like this:
>
> N H1 H2 H3 CA HA CB HB2 HB3 OG HG C O
>
> and in your PDB file it is ordered like this, with the order of the
> hydrogen atoms reversed:
>
> N
> H3
> H2
> H1
> CA
> HA
> CB
> HB3
> HB2
> OG
> HG
> C
> O
>
> this is OK for LCPO, because the order of the heavy atoms still matches.
>
>> Is there a way to change atom order in prmtop? (Because it seems that
>> conversion of PDB is much less straightforward.)
>
> The atom order in the prmtop is based on whatever residue templates
> are read in by leap from force field data, and you probably don't want
> to go modifying that. If your heavy atoms are out of order you could
> potentially try using the 'atommap' command in cpptraj to reorder the
> PDB so that its atom order matches the amber parm, although I'm not
> sure how well that will work since atommap was really only intended
> for use with smaller ligands (<100 atoms); I haven't really tested it
> on protein-like structures. Here is some example input that reorders a
> PDB file (xtallig.pdb) so that it matches an Amber Topology/restart
> (start.parm7/start.rst7):
>
> parm xtallig.pdb
> reference xtallig.pdb
> parm start.parm7
> reference start.rst7 parmindex 1
> atommap xtallig.pdb start.rst7 mapout atommap.dat
> trajin xtallig.pdb
> trajout reordered.xtallig.pdb pdb
>
> Hope this helps,
>
> -Dan
>
>>
>> Dmitry
>>
>> On 03/15/2012 08:46 PM, Daniel Roe wrote:
>>> 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
>>>>
>>>>
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>>>
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>>
>> --
>> 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
>>
>>
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>
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-- 
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



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Received on Fri Mar 16 2012 - 09:30:02 PDT
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