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

From: Elvis Martis <>
Date: Tue, 9 May 2017 04:11:43 +0000

If GAFF or GAFF2 does not have parameters for your molecule the "frcmod" file supplies the parameters.
If you do not give a value and only mention the atoms, then I guess leap takes "0" as a value.
You must be very careful with this.
    Best Regards

Elvis Martis
Ph.D. Student (Computational Chemistry)
 at Bombay College of Pharmacy

A  Kalina, Santacruz [E], Mumbai 400098, INDIA
Skype. adrian_elvis12

-----Original Message-----
From: p.kartheek []
Sent: Monday, May 08, 2017 11:04 PM
Subject: [AMBER] tleap-incorpoarating .frcmod, .prep files for unnatural nucleotides

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 "". 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 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 "MASS 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, 9701577399,, _______________________________________________
AMBER mailing list

AMBER mailing list
Received on Mon May 08 2017 - 21:30:02 PDT
Custom Search