Dear Amber community,
While I was trying to make a solvent box,
I realise that there where some parameters missed.
In my case was the force constant and the angle for a H-C-Br,
In order to obtain the values, I did import gaff (source leaprc.gaff),
however those values are not there.
After some time I did fine the values I was looking, and did what I had to do.
So,Today, I decide to have a look through the gaff.dat file. For my surprise,
I did find the "missed" values there.
My question is, what is the correct form to import gaff and the other sources?
What could be the mistake in my case?
is there other form to use the data in gaff ?
This is part of the output in the terminal, as you can see,
it imported gaff successfully. !!
tleap -f act
-I: Adding /opt/AMBER/amber14/dat/leap/prep to search path.
-I: Adding /opt/AMBER/amber14/dat/leap/lib to search path.
-I: Adding /opt/AMBER/amber14/dat/leap/parm to search path.
-I: Adding /opt/AMBER/amber14/dat/leap/cmd to search path.
-f: Source act.
Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./act
Loading parameters: /opt/AMBER/amber14/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008)
----- Source: /opt/AMBER/amber14/dat/leap/cmd/leaprc.gaff
----- Source of /opt/AMBER/amber14/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /opt/AMBER/amber14/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.7, Nov 2013)
----- Source: /opt/AMBER/amber14/dat/leap/cmd/leaprc.ff12SB
----- Source of /opt/AMBER/amber14/dat/leap/cmd/leaprc.ff12SB done
Log file: ./leap.log
Loading parameters: ./br.frcmod
Reading force field modification type file (frcmod)
Reading title:
BROMO parms
Loading Mol2 file: ./dbr.mol2
Reading MOLECULE named DIB
Checking 'dibr'....
Checking parameters for unit 'dibr'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
Finally I did compare force constant values,
H-C-Br 43.18 in the gaff file
H-C-Br 48.61 the one that I did found.
What is the real impact of those 5.43 kcal/mol(A)2 difference?
Is there any form to calculate a force constant for a specific bond in AMBER?
(maybe paramfit)
Thanks in advance
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Received on Fri Aug 12 2016 - 06:30:03 PDT
