[gmx-users] dna-protein simulation

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 24 12:56:10 CEST 2008

prasun kumar wrote:
> Hello Tsjerk,
> while running pdb2gmx I was getting error like
> h1 is not found while assigning improper dihedral
> so I just modified the forcefield(ffG43a1.rtp)file by default it was 
> considering ADE also inplace of considering DADE part only,so I removed 
> ADE,CYT,GUA part also(is it right to do so?)

You shouldn't have to do this.  You should be able to re-name each residue in 
the .pdb file to agree with with nomenclature in the .rtp file.

Before addressing the problems below, I would suggest you go back and fix these 
initial steps.  If you're getting too creative at the pdb2gmx step, probably 
something is wrong :)

> after that I am not getting any error in this step.
> Now the topology file that is generated is not having angle type and 
> dihedral type

If the topology is incomplete, something has gone wrong.  I would stop right 
here and evaluate the initial pdb2gmx step (see above).


> for example:
> 1.18   19    20(which is nothing but the angle betwen OA   P   OM)
> 2.18   19    22(OA    P     OA)
> 3.17   18   19   20(CH1  OA   P   OM)
> 4.18   19   22   23(OA      P    OA   CH2)
> then I searched in the ffG43a1bon.itp and get the values llike(I guess 
> it is correct,you please give your suggestion)
> 1. ga_13(its given for OM   P   OA)
> 2.ga_4  (given for same)
> 3.gd_9  &  gd_11 (given for -OA-P-)
> I added these values to the topology file.It makes the grompp command 
> running
> I minimized the structure also but the problem I am facing is following:
> Fatal error:
> Group other not found in indexfile.
> Maybe you have non-default goups in your mdp file, while not using the 
> '-n' option of grompp.
> In that case use the '-n' option.
> Actually gromacs is not recognizing the DNA molecule.while running 
> genbox command I found the following:
> system is having
> 1687 :other residue(4 dna and 1683 water molecule)
> 0:protein
> 0:dna
> Now what should I do?
> I am sure that I am doin something wrong in the beginning itself
> can you please help me in identifying that error or can you please send 
> me a sample pdb file having dna molecules
> with regards
> -- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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