Hi Dan,
I have successfully converted pdb to prmtop, and surf works now, but
cpptraj complains about the atom order in pdb and prmtop files in such
style:
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?
Is there a way to change atom order in prmtop? (Because it seems that
conversion of PDB is much less straightforward.)
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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>> 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 - 08:30:03 PDT
