On 2/14/13 4:15 PM, Abhishek Acharya wrote:
Hello Justin
Thank you very much for your effort and help. I will try adding new
parameter corresponding to the errors. Meanwhile just out of curiosity and
possible need, what should be done in case no matching parameters are
found for the missing dihedrals? I see that there are 6 fields in the
dihedrals section of ffbonded.itp. How do we calculate these parameters
for new dihedrals ?
I wanted to go step by step. I first tried to address the errors 1, 2 and
3. So I added the following dihedrals to ffbonded.itp.
For Error1:
HC CT CT NA 3 -4.09614 5.08775 2.96645 -3.95806
0.00000 0.00000
from:
HC CT CT NT 3 -4.09614 5.08775 2.96645 -3.95806
0.00000 0.00000 ; amine all-atom
For Error2
OH CT CT NA 3 9.89307 -4.71746 3.67774 -8.85335
0.00000 0.00000
from:
N3 CT_2 CT OH 3 9.89307 -4.71746 3.67774 -8.85335
0.00000 0.00000 ; Chi for Ser & Thr
For Error3
CT OS CT NA 3 -5.23000 7.32200 6.27600 -8.36800
0.00000 0.00000
from:
CT OS CT N 3 -5.23000 7.32200 6.27600 -8.36800
0.00000 0.00000 ; (From wildcard) imidazoles, indoles, purines
I expected this to remove the errors 1, 2 and 3. I took care to keep the
atomtypes order the same. But this doesn't seem to affect the result. I
get the same errors. Any ideas??
None. If you add new parameters in the right directive, the errors will go
away. I can offer no explanation as to why that's failing here. You can, of
course, enter all the missing parameters directly into the topology rather than
having them looked up from ffbonded.itp, but that really shouldn't be necessary.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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