[gmx-users] pdb2gmx + non-protein

[David]

On Thu, 2003-01-30 at 20:27, Alberto Imparato wrote:
> Hi All
> I'm trying to obtain a topology file starting from a very simple .gro
> file, using pdb2gmx .
> My 2_dppc.gro file contains 2 DPPC molecules, each containing 50 atoms:
> 
> DPPC
>   100
>     1DPPC  C1  1   1.305  0.021  4.907   -0.4017   -0.1211   -0.18
>     1DPPC  C2  2   1.345  0.856  4.733   -0.171   -0.6351   -0.2036
>     1DPPC  C3  3   1.191  0.812  4.904   0.1336   0.3719   0.2801
>     1DPPC  N4  4   1.244  0.919  4.819   -0.0492   -0.1049   -0.4439
>     1DPPC  C5  5   1.131  0.985  4.751   -0.7172   -0.308   0.4587
>     ....
>     ....
>     2DPPC  C1  51   1.305  0.021  0.093   -0.4017   -0.1211   -0.18
>     2DPPC  C2  52   1.345  0.856  0.267   -0.171   -0.6351   -0.2036
>     2DPPC  C3  53   1.191  0.812  0.096   0.1336   0.3719   0.2801
>     2DPPC  N4  54   1.244  0.919  0.181   -0.0492   -0.1049   -0.4439
>     2DPPC  C5  55   1.131  0.985  0.249   -0.7172   -0.308   0.4587
>     ....
>     ....
> 

> WHY the 2 molecules are not recognized as DPPC molecules, but are treated
> as 1 single Protein ???

pdb2gmx only works for residue types that are present in the database.
DPPC is not. Check Peter Tieleman's website.

> The same happens when I first transform 2_dppc.gro to  2_dppc.pdb using
> editconf and the process the latter file with pdb2gmx.
> Thak you
> Alberto
> 
> 
> 
> 
> 
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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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