[AMBER] tleap-incorpoarating .frcmod, .prep files for unnatural nucleotides

From: p.kartheek <kartheekpitta.gmail.com>
Date: Mon, 8 May 2017 23:03:43 +0530

Dear Amber users,
I am naive to amber tleap. Trying to generate topology files for
8-oxoguanine. 8OG.prep and 8OG.frcmod files were downloaded from "
http://research.bmh.manchester.ac.uk/bryce/amber". However, I am puzzled to
incorporate these frcmod and prep files in tleap. After playing around with
it, I have come up with two strategies of error free incorporation methods.
           In method 1, I will parsing the tleap -f leap.in by adding a
line "NONB" at the end of the file. In method 2, I will directly copy the
contents of .frcmod file into leaprc.DNA.bsc1 into their respective bonded,
angle,improper and propers dihedrals sections.
I am able to generate topologies by following either method, however I
feel editing leaprc.DNA.bsc1 would be very inappropriate as any mistake may
develop some serious issues. After doing little inspection through the file
leaprc.DNA.bsc1, I have noticed that the file is starting with
CI 12.01"

for which at the end of the file NONB term is added

CI 1.9080 0.1094"

However in my 8OG frcmod file

DH 1.0"

is given and "NONB" term at the end of file is missing, after
incorporating "NONB" at the end of the file I am able to generate
topologies without any errors.
Is it necessary to write exact values in the NONB section of frcmod file if
not how those values will be taken care ?.

Please guide me through the right path. Any help would be highly
appreciated, thanks for your patience.

source /home/kartheek/amber16/dat/leap/cmd/leaprc.DNA.bsc1
source /home/kartheek/amber16/dat/leap/cmd/leaprc.water.tip3p
source /home/kartheek/amber16/dat/leap/cmd/leaprc.gaff2
loadamberparams 8OG.frcmod
loadamberprep 8OG.prep
bdna=loadpdb "eq8og_noh.pdb"
saveamberparm bdna eq8og.prmtop eq8og.inpcrd
savepdb bdna eq8og_amber.pdb
P. Kartheek,
PhD Candidate, Computational Biophysical Chemistry,
Center for Computational Natural Sciences and Bioinformatics,
International Institute of Information Technology,
Marimuthu Krishan Group,
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Received on Mon May 08 2017 - 11:00:02 PDT
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