[gmx-users] Self made GDP topology file
Daan van Aalten
vdava at davapc1.bioch.dundee.ac.uk
Mon Nov 8 09:09:01 CET 2004
Just another reminder that you cannot use the current (ffgmx-based) PRODRG
topologies for the more recent force fields - I am sure the molecules will
"deform" as you are using the constants/forces in the wrong context.
On Fri, 5 Nov 2004, Zhenting Gao wrote:
> Hi Bert,
> I tried the 'raw' PRODRG topology, it deformed. So I turned to modify the topology myself.
> My college once met the similar problem about ATP. He first uses the PRODRG topology but failed in the EM process. However he is lucky because later he find there is ATP in GMX's rtp file. And he used the output topology of ATP by pdb2gmx.
> BTW: would you please to suggest some basic references of Essential Dynamics for me, because I want to simulate a protein with allosteric change between 2 domains.
> ======= 2004-11-04, 19:15:40 2004-11-04, 19:15:40 you wrote：=======
> >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
> = = = = = = = = = = = = = = = = = = = =
> Yours sincerely,
> Zhenting Gao
> zhentg at 163.com
> Drug Discovery and Design Center,
> Shanghai Institute of Materia Medica,
> Chinese Academy of Science
> P.R. China
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