[gmx-users] Rotated protein

[Shima Arasteh]

Thanks dear Erik.


 
Sincerely,
Shima


----- Original Message -----
From: Erik Marklund <erikm at xray.bmc.uu.se>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Monday, September 17, 2012 2:05 PM
Subject: Re: [gmx-users] Rotated protein

Hi,

Your pdb input (protein.pdb) is misformatted. Note that a pdb file is fix-format and that your residue sequence number is misaligned. As a consequence the last digit is not read for two digit residues.

Erik

15 sep 2012 kl. 07.56 skrev Shima Arasteh:

> Sorry for unclear explanation.
> 
> 1. First step:
>     editconf -princ -rotate 0 60 0 -f protein.pdb -o protein-rotate.gro
> 2.    Second step:
>     editconf -f protein-rotate.gro -o protein-rotate.pdb
> 
> Some lines of protein.pdb are :
> ATOM     59  CB  PHE     9      -7.899   7.143  -7.348  1.00  0.00              
> ATOM     60  CG  PHE     9      -8.253   5.762  -7.846  1.00  0.00              
> ATOM     61  CD1 PHE     9      -8.061   5.433  -9.193  1.00  0.00              
> ATOM     62  CD2 PHE     9      -8.775   4.811  -6.960  1.00  0.00              
> ATOM     63  CE1 PHE     9      -8.389   4.152  -9.654  1.00  0.00              
> ATOM     64  CE2 PHE     9      -9.103   3.530  -7.422  1.00  0.00              
> ATOM     65  CZ  PHE     9      -8.910   3.201  -8.768  1.00  0.00              
> ATOM     66  N   SER     10     -8.048   5.490  -4.333  1.00  0.00              
> ATOM     67  CA  SER     10     -7.399   4.461  -3.545  1.00  0.00              
> ATOM     68  C   SER     10     -7.862   3.074  -3.967  1.00  0.00              
> ATOM     69  O   SER     10     -9.048   2.763  -3.893  1.00  0.00              
> ATOM     70  CB  SER     10     -7.715   4.626  -2.061  1.00  0.00  

-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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