[gmx-users] Self made GDP topology file.......deforms severely with LINC warning during EM and stopped

Bert de Groot bgroot at gwdg.de
Thu Nov 4 19:15:40 CET 2004

Zhenting Gao wrote:
> Hi  gmx-users,                                
>      A GDP is in my protein complex. So I made my own Gromos 96 FF topology file for GDP.   
>      First, I get the topology from PRODRG server.   
>      Then I use Gaussian to recalculate the atom charge.   
>      At last I refer to the topology of ATP and GUA in ffG43a1.rtp to modify the topology file for GDP.   
>      However, the GDP deforms severely during the EM, and even crashes if I run a heating process.(it deforms whether I add positive ion or not. ) 
>      In contrast, the topology files generated by pdb2gmx for ATP and DGUA  make the structure ramain good during a 300K heating process. 
>      Why it deforms? It is the wrong force parameter? Or the wrong atom charge? 

Hi Zhenting,

did you check if you also get the deformation with the "raw" PRODRG topology?
If not, then I'd check step by step where your hand-made updates differ from the
PRODRG suggestion and how they relate to the deformation.

If yes, ask the PRODRG developers ;-)



Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302

email: bgroot at gwdg.de

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