[gmx-users] dna-protein simulation
prasun30 at gmail.com
Fri Sep 26 02:56:32 CEST 2008
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
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:
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
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