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

Matthew Geballe mgeball at emory.edu
Tue Nov 9 20:02:37 CET 2004


I too have been trying to build a topology for both GDP and GTP.  I did 
this in generally the same way that you describe, starting from PRODRG 
output and looking at the ATP and GUA residues in the G43a1 residue 
database.  Rather than calculating charges I generally used the charges 
from the residue database with a few minor changes.  My topologies seem 
to be stable in MD simulations, although I have a problem with the 
beta-phosphate group of GDP.  I'd be happy to send the topologies to 
you and any improvements you or any one else would like to make would 
be greatly appreciated.


P.S.  According to an earlier post, it sounds like PRODRG will soon 
support the G96 force field thanks to much hard work by Daan van Aalten 
and others.  Thanks in advance for expanding your great tool!!

On Nov 9, 2004, at 1:56 AM, Zhenting Gao wrote:

> Hi  gmx-users,
>      Sorry, I have sent several mails with unreadable chraracters to 
> the maillist due to my email client software.
>      And thanks for the kind replies.
>      Luckily, after days of struggle, I find the reason of the 
> deformation. Hereafter I repeat the problem first.
>      A GDP is in my protein complex.
>      I choose Gromos 96FF to do MD, and made my own GDP topology file 
> in Gromos 96 FF.
>      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.
>      To validate the topology file for GDP, I included the GDP in a 
> water box and performed a 20 ps EM and heating.
>      However, the GDP deforms severely during the EM, and even crashes 
> if I run a heating process.(it deforms whether I add ions or not.)
>      In contrast, the topology files generated by pdb2gmx for ATP, GUA 
> 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?
>      I did a comparison of the definition of atom, bonds, angles, 
> dihedrals between my GDP toplogy and the GUA topology in the 
> ffG43a1.rtp.
>      And I find out that
>           1.every thing is the same(almost) except the difference of 
> atom charges
>           2.charge difference of atoms that deform the structure(C2, 
> N2, N3, N1) is very large(C2 0.715, N2 0.354, N3 0.462, N1 0.511).
>      Furthermore, I modified the GDP atom charge acoording to the GUA 
> and ATP and did a 2ns heating(300K), the structure remain intact.
>      So I believe it is the charge that caused the deformation.
>      I searched this maillist, and find some similar questions about 
> the charge calculation.
>      http://www.gromacs.org/pipermail/gmx-users/2003-August/006691.html
> http://www.gromacs.org/pipermail/gmx-users/2003-September/006970.html
>     It seems that QM(e.g. 'CHELPG' or 'Merz-Kollman' methods in 
> Gaussian) charges are too big in some cases.Though the 'big' charge 
> may not result in a deformation( my collegues use QM charges well), 
> they are not appropriate in the cases of ATP, ADP and GDP.( My 
> collegues found before that self made topology for ADP and ATP with QM 
> charges also defrom.
> http://www.gromacs.org/pipermail/gmx-users/2004-March/009747.html).
>      Everyone should know that the atom charge is really important for 
> an MD simulation; the QM charge may not be the best choice.
>      And I really expect that someone can give details in how to 
> calculate the atom charge for gromacs topology.
>      Best wishes.
> Yours sincerely,
> Zhenting Gao
> zhentg at 163.com
> 2004-11-9
> ------------------------------------
> Drug Discovery and Design Center,
> Shanghai Institute of Materia Medica,
> Chinese Academy of Science
> P.R. China
> http://www.dddc.ac.cn/group/zhentg.htm
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Matthew T. Geballe
Graduate Student
Department of Chemistry
Emory University
1515 Dickey Drive
Atlanta, GA 30322

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