[gmx-users] Re: Self made GDP topology file....deforms during EM...and the reason

Ruben M Buey ruben at akilonia.cib.csic.es
Fri Nov 12 12:57:30 CET 2004

We have also used a GTP and GDP topology for G96 ff and it seems to be 
stable during the simulations. I can send both of you the files if you 
wish, just to compare, check and try to improve (if it´s possible...)

Zhenting Gao wrote:

>Hi Matt,  
>     I am happy to know that we get the topology for GDP in similar way. However, I use MMFF94 charge(generated in Sybyl) in my topology file. It is stable during a 20ps run. And I am running a 2ns test now.  
>     It is nice of you to send me your topology.(zhentg at 163.com)  
>     I still wonder how GMX developer calcute charges for the entries in the GMX database.  
>     Also, I am longing for Daan van Aalten to release a new PRODRG service for GMX users.  
>Yours sincerely,  
>Zhenting Gao  
>Drug Discovery and Design Center,    
>Shanghai Institute of Materia Medica,   
>Chinese Academy of Science  
>P.R. China  
>gmx-users mailing list
>gmx-users at gromacs.org
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.

Ruben M Buey. PhD student. Lab 308
Centro de Investigaciones Biologicas
Consejo Superior de Investigaciones Cientificas
Dpt. Protein Function and Structure
C/ Ramiro de Maeztu, 9 
28040  Madrid   (SPAIN)
Phone:   34-918373112 ext 4380
Fax:     34-915360432

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