[gmx-users] dna-protein simulation

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Sep 27 13:46:33 CEST 2008

Hi Prasun,

It was already pointed out that you shouldn't change the names in the
force field files. ADE stands for RNA-Adenine and DADE stands for
DNA-Adenine, keep it that way! Change the PDB file instead, but do it
properly. So, do a restart:

Take the original pdb file.
Check the residue names, atom names and atom order of the bases in the
force field files.
Change the pdb file according to this, but do mind the pdb file
format. Check the specifications, which can be found on the rcsb page.



On Fri, Sep 26, 2008 at 2:56 AM, prasun kumar <prasun30 at gmail.com> 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?)
> 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
> 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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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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