[AMBER] ptraj removes my ligands

From: DENILSON FERREIRA DE OLIVEIRA <denilson.dqi.ufla.br>
Date: Mon, 26 Mar 2012 23:22:48 -0300 (BRT)

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 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 Mon Mar 26 2012 - 19:30:02 PDT
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