lina wrote:
pdb2gmx -ter
I doubt this is of any use; the Amber force fields don't use the same
conventional termini selection that the other force fields do, as the OP states.
I suspect that's why the .tdb approach is not working.
I think the best approach is to simply write .rtp entries for the modified
terminal residues with unique names such that they are distinguished from all
other residues. I don't know if it will work (since termini in Amber are
treated differently), but it's worth a try.
-Justin
On Sat, Aug 27, 2011 at 6:17 PM, Vijayaraj <vijayara...@gmail.com> wrote:
Hello,
I am using gromacs 4.5.4 with amber99sb ff. I would like to modify the
terminal residues from NALA and CALA to normal ALA (just as middle
residues). As the terminal selection option is not enabled with the amber
ff, I am using the termini modification parameters with aminoacids.c.tdb.
here is my code for the aminoacids.c.tdb
[ COO- ]
[ replace ]
H H 1.00800 0.27190
N N 14.01000 -0.41570
CA CT 12.01000 0.03370
HA H1 1.00800 0.08230
C C 12.01000 0.59730
CB CT 12.01 -0.1825
HB1 HC 1.008 0.0603
HB2 HC 1.008 0.0603
HB3 HC 1.008 0.0603
[ add ]
1 1 O C CA N
O 16.00000 -0.56790
[ bonds ]
C O 1 0.12290 476976.0
[ delete ]
OC1
OC2
when I run pdb2gmx using this termini modification, everything works fine
except the deletion of OC1 and OC2 atoms, the error which I get for this run
as follows,
Fatal error:
Atom OC2 not found in residue seq.nr. 8 while adding atom
any suggestion to delete the OC1 and OC2 atoms. If I dont enable this [
delete ] option with the aminoacids.c.tdb file, it works fine by adding the
O atom to the terminal residue including the presence of OC1 and OC2 atoms.
first I am trying to modify the c terminal residue.
Regards,
vijay.
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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