[gmx-users] dna-protein simulation

prasun kumar prasun30 at gmail.com
Wed Sep 24 07:34:20 CEST 2008

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
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)

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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