AMBER Archive (2006)

Subject: Re: AMBER: mask issues

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Tue Feb 28 2006 - 07:03:16 CST

Dear Claire,

To me the scripts look OK... Hope I didnt ovelooked something!!
It would be useful to see also the ptraj log files and the error
messages... otherwise I am afraid there is not much to tell .... You
should either post your error messages or check them throughoutly to see
what exactly is wrong .. Generally, ptraj log files are good in
indicating where the problems might be ...

Vlad

Claire Zerafa wrote:

> Hello all..
>
> I am trying to carry out some pca analysis and am doing some
> preparatory work in ptraj. I am interested in my active site residues,
> and then in the CA atoms of my active site residues. I prepared two
> sets of command lines as follows:
>
> PTRAJ 1 Active Site RESIDUES
>
> trajin /DATA/1e3g_wat_md2.mdcrd.gz
> trajin /DATA/1e3g_wat_md3.mdcrd.gz
> trajin /DATA/1e3g_wat_md4.mdcrd.gz
> trajin /DATA/1e3g_wat_md5.mdcrd.gz
> trajin /DATA/1e3g_wat_md6.mdcrd.gz
> trajin /DATA/1e3g_wat_md7.mdcrd.gz
> trajin /DATA/1e3g_wat_md8.mdcrd.gz
> trajin /DATA/1e3g_wat_md9.mdcrd.gz
> trajin /DATA/1e3g_wat_md10.mdcrd.gz
> rms first out /DATA/undocked_rms1_as.out
> :33,36,37,39,40,43,73,74,77,78,81,84,96,112,119,205,208,209,212,223,227,231
>
> average /DATA/undocked_average_output_as.pdb pdb nowrap
> go
>
> PTRAJ2 Active Site RESIDUES
>
> trajin /DATA/1e3g_wat_md2.mdcrd.gz
> trajin /DATA/1e3g_wat_md3.mdcrd.gz
> trajin /DATA/1e3g_wat_md4.mdcrd.gz
> trajin /DATA/1e3g_wat_md5.mdcrd.gz
> trajin /DATA/1e3g_wat_md6.mdcrd.gz
> trajin /DATA/1e3g_wat_md7.mdcrd.gz
> trajin /DATA/1e3g_wat_md8.mdcrd.gz
> trajin /DATA/1e3g_wat_md9.mdcrd.gz
> trajin /DATA/1e3g_wat_md10.mdcrd.gz
> reference /DATA/undocked_average_output_as.pdb
> rms first out /DATA/undocked_rms2_as.out
> :33,36,37,39,40,43,73,74,77,78,81,84,96,112,119,205,208,209,212,223,227,231
>
> strip
> ~:33,36,37,39,40,43,73,74,77,78,81,84,96,112,119,205,208,209,212,223,227,231
>
> trajout /DATA/undocked_rms2.out_as.mdcrd
> go
>
> PTRAJ 1a Active Site RESIDUES CA ONLY
>
>
> trajin /DATA/1e3g_wat_md2.mdcrd.gz
> trajin /DATA/1e3g_wat_md3.mdcrd.gz
> trajin /DATA/1e3g_wat_md4.mdcrd.gz
> trajin /DATA/1e3g_wat_md5.mdcrd.gz
> trajin /DATA/1e3g_wat_md6.mdcrd.gz
> trajin /DATA/1e3g_wat_md7.mdcrd.gz
> trajin /DATA/1e3g_wat_md8.mdcrd.gz
> trajin /DATA/1e3g_wat_md9.mdcrd.gz
> trajin /DATA/1e3g_wat_md10.mdcrd.gz
> rms first out /DATA/undocked_rms1_as_CA.out
> :33,36,37,39,40,43,73,74,77,78,81,84,96,112,119,205,208,209,212,223,227,231_at_CA
>
> average /DATA/undocked_average_output_as_CA.pdb pdb nowrap
> go
>
>
> PTRAJ 2a Active Site RESIDUES CA ONLY
>
>
> trajin /DATA/1e3g_wat_md2.mdcrd.gz
> trajin /DATA/1e3g_wat_md3.mdcrd.gz
> trajin /DATA/1e3g_wat_md4.mdcrd.gz
> trajin /DATA/1e3g_wat_md5.mdcrd.gz
> trajin /DATA/1e3g_wat_md6.mdcrd.gz
> trajin /DATA/1e3g_wat_md7.mdcrd.gz
> trajin /DATA/1e3g_wat_md8.mdcrd.gz
> trajin /DATA/1e3g_wat_md9.mdcrd.gz
> trajin /DATA/1e3g_wat_md10.mdcrd.gz
> reference /DATA/undocked_average_output_as.pdb
> rms first out /DATA/undocked_rms2_as_CA.out
> :33,36,37,39,40,43,73,74,77,78,81,84,96,112,119,205,208,209,212,223,227,231_at_CA
>
> strip
> ~:33,36,37,39,40,43,73,74,77,78,81,84,96,112,119,205,208,209,212,223,227,231_at_CA
>
> trajout /DATA/undocked_rms2.out_as_CA.mdcrd
> go
>
> In the first set PTRAJ 1 & 2 I am working on the entire amino acids
> making up the active site. In the second set PTRAJ 1a & 2a I am
> working on the alpha carbons of the amino acids making up the active
> site. For both cases, in ptraj 1 I generate an average pdb for my
> trajectory, which acts as a reference in ptraj 2 when I fix each
> trajectory frame to the first (or reference). I must have some problem
> in assigning my mask, because when I continue further I get error
> messages. In PTRAJ 1 & 2 I am selecting for the residues hence the use
> of :33,36,37 etc and then in PTRAJ 1a & 2a I am selecting for the CA
> of these residues- hence the @CA after the residues being considered.
>
> Can anyone tell me what is wrong with my script files please?
>
> Thanks in advance
>
> claire
>
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-- 
Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/

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