Dear Amber Users,
I want to simulate a DNA structure (DNAzyme) with a nick ( 5'
three-phosphate) inside the structure. I introduced a nick and add
three-phosphate to the Guanine, then I followed the standard procedure
with *antechamber
*to generate *library *and *frcmod * for this three-phosphate Guanine.
These file have been successfully generated and then I used these files
for generating parameter topology and input coordination for the whole
DNAzyme structure.
Unfortunately I got the " atoms not in residue templates" error from the
xleap for the P and O atoms.
I tried different name for phosphate and oxygen as below:
Alpha-beta-gamma phosphate
PA
O1A
O2A
PB
O1B
O2B
PG
O1G
O2G
O3G
and also use plain P or O
P
OP1
OP2
..
.
but non of them helped me to solve the problem.
I used Hyperchem to add three-phosphate to Guanine residue, so I edited
these name according to standard names.
Is there any standard method for nomenclature of Phosphate and Oxygen
groups?
Should I use Chimera to generate there files or is there any procedure to
solve these phosphate-type-errors?
Any help would be greatly appreciated.
Regards,
M. Reza
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Received on Fri May 27 2016 - 01:30:04 PDT
