[gmx-users] pdb2gmx problem

[David]

On Wed, 2003-05-21 at 08:33, Vivek Raut wrote:
> following is the .pdb file i give as input:
> 
> REMARK   4 
> 
> REMARK   4 LYSI COMPLIES WITH FORMAT V. 2.0, 
> 20-MAY-2003
> ATOM      1  C   MTYL     1      7.844  -6.601  -8.462  0.00  0.00 
>   C
> ATOM      2  C   MTYL     1      3.503  -6.594  -5.983  0.00  0.00 
>   C

> 
> The residue type is added in ffgmx.rtp file as:
> 
> [ MTYL ]
>   [ atoms ]
>     C    C       0.01    1


If I understand you correctly your residue has only one atom. In that
case you probably want to give all MTYL a different residue number in
the input file

> but after using pdb2gmx, in output I see:
> 
> 1MTYL     C    1   0.784  -0.660  -0.846
>      2MTYL     C    2   0.350  -0.659  -0.598
>      3MTYL     C    3   0.782  -0.668  -0.346
>      4LYSH     N    4   0.122   0.500   0.600
>      4LYSH    H1    5   0.042   0.490   0.541
>      4LYSH    H2    6   0.101   0.561   0.676
>      4LYSH    H3    7   0.198   0.538   0.547
>      4LYSH    CA    8   0.268   0.000   0.800
>      4LYSH    CB    9   0.329   0.500   0.300
>      4LYSH    CG   10   0.485   0.100   0.900
>      4LYSH    CD   11   0.548   0.900  -0.115
>      4LYSH    CE   12   0.701   0.900   0.600
>      4LYSH    NZ   13   0.763   0.000   0.200
>      4LYSH   HZ1   14   0.789  -0.066   0.270
>      4LYSH   HZ2   15   0.674  -0.026   0.161
>      4LYSH   HZ3   16   0.832   0.000   0.128
>      4LYSH     C   17   0.321   0.219   0.800
>      4LYSH    O1   18   0.242   0.302   0.726
>      4LYSH    O2   19   0.429   0.256   0.874
> 
> it reads only 2 MTYL atoms & ignores other 18. Also the coordinates are 
> also changed. Why so?... & how do i rectify it?
> 
> -------------------------------------------------------------------------------------------------------------------------------------------
> Vivek Raut
> Graduate Research Assistant
> Department of Bioengineering
> Clemson University
> Clemson, SC- 29631. USA
> Email: vraut at clemson.edu
> Phone: 864-650-1431
> --------------------------------------------------------------------------------------------------------------------------------------------
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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