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
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
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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 - 09:00:02 PDT
