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

[Bert de Groot]

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 ;-)

cheers,


Bert

____________________________________________________________________________
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
http://www.mpibpc.gwdg.de/abteilungen/073
____________________________________________________________________________