OK.
Thank you.
Best wishes.
Denilson
--------------------------------------------------
From: "Daniel Roe" <daniel.r.roe.gmail.com>
Sent: Friday, March 30, 2012 3:36 PM
To: "AMBER Mailing List" <amber.ambermd.org>
Subject: Re: [AMBER] ptraj removes my ligands
> Hi,
>
> I notice that in both your PDB and PSF files the residue numbers reset
> when they get to the SAH/CHA residues, and that SAH and CHA have the
> same residue number (1). If I manually change the resnum of SAH to 0
> (so that SAH and CHA have different residue numbers) it seems to work
> fine, so I think ptraj just gets a bit confused by this non-standard
> formatting. The same issue (idential resnums) occurs with the second
> set of files.
>
> I suppose we should have a check when reading in PDB/PSF files that
> checks for residue name changes within the same residue number.
> Anyway, thanks for the report!
>
> -Dan
>
> On Mon, Mar 26, 2012 at 10:22 PM, DENILSON FERREIRA DE OLIVEIRA
> <denilson.dqi.ufla.br> wrote:
>> Dear all,
>>
>> I have got a protein with two chains, two cofactors, two ligand molecules
>> named CHA, water and chloride ions in my files. I submitted my system to
>> a molecular dynamics simulation using Namd with charm force field and now
>> I want to convert the dcd file in charmm format to the amber trj format
>> using ptraj (Ambertools 1.5, compiled with gnu 4.6.1, in a ubuntu 11.10
>> machine). Consequently, I used the following command:
>>
>> ptraj DIM_SAH_CHA_4_all.psf ptrajfile.in
>>
>> The commands in ptrajfile.in are:
>>
>> trajin cc_DIM_SAH_CHA_4_all.dcd 800 1000 1
>> strip :CLA
>> strip :TIP3
>> trajout 800_1000.trj nobox
>> average media.pdb pdb
>>
>> Although the program seems to work perfectly, the generated pdb file
>> (media.pdb) does not contain my ligands (CHA).
>>
>> Initially I thought that the problem could be my dcd file. Thus, I used a
>> pdb file instead. In this case the commands in the ptrajfile.in were:
>>
>> trajin DIM_SAH_CHA_4_all.pdb
>> strip :CLA
>> strip :TIP3
>> trajout 800_1000.trj nobox
>> average media.pdb pdb
>>
>> Again, ptraj removed my ligands (CHA). Apparently the problem occurs when
>> the program reads my psf file because on the screen CHA does not appears
>> among the list of residues the program finds in the psf file. I have done
>> some tests using VMD 1.9.1 to check my files (pdb, psf and dcd), but I
>> could not find any problem. Consequenly, it seems to be a bug in ptraj.
>> Anyway, I would appreciate if somebody could be kind enough to help me.
>>
>> Best regards.
>>
>> Denilson.
>>
>> Denilson F. OliveiraLaboratório de Produtos NaturaisDepartamento de
>> QuímicaUniversidade Federal de LavrasCaixa Postal 3037Lavras - MG -
>> BrasilCEP 37.200-000Tel: (55)(35) 3829-1623Fax: (55)(35) 3829-1271e-mail:
>> denilson.dqi.ufla.br
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Apr 02 2012 - 07:00:07 PDT
