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).
-Justin
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
--
PRASUN (ASHOKA)
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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