Yeah I was afraid of that - the algorithm was really only intended for
remapping small ligands.
If you can give me one frame of your PDB file I can use the soon-to-be
released version of Cpptraj (V12) to convert it to a mol2 with bond
information, which you can then use as a parm for your PDB file to
calculate LCPO SA.
-Dan
2012/3/16 Dmitry Osolodkin <divanych.rambler.ru>:
> 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
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>> --
>>> 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
>
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Mar 16 2012 - 10:00:03 PDT
