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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Received on Fri Mar 30 2012 - 12:00:04 PDT
