the parameters of my molecule were obtained from gaff since i used antechamber.
Does this mean as you mentionned, my prmtop file will not contain vdw for n3 and
n? so I should add them in an additional frcmod file?
Also I want to printout the global frcmod (to be sure what is considered
exactly by the code) file for my residues built with antechamber, using command:
$AMBERHOME/exe/parmchk -i cen.prepin -f prepi -o cen.frcmod -a Y
(I added -a Y) but nothing happened.
Another question, where do I find please the definition on how types have been
assigned in gaff, exple n3, n2 n etc?
Thanks a lot
for your help with this
________________________________
From: Thomas Cheatham III <tec3.utah.edu>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Tue, August 3, 2010 10:11:58 PM
Subject: Re: [AMBER] RDPARM
> Type r* eps
> n1 1.8240 0.1700
> c3 1.9080 0.1094
> h1 1.3870 0.0157
> hn 0.6000 0.0157
> c2 1.9080 0.0860
> o 1.6612 0.2100
> hc 1.4870 0.0157
> ha 1.4590 0.0150
>
> There are type n, and n3 that are missing.
If you look at the parm files, i.e. parm99.dat you will see near the
bottom (where the vdw parameters are):
N NA N2 N* NC NB NT NY
C* CA CB CC CD CK CM CN CQ CR CV CW CY CZ
MOD4 RE
H 0.6000 0.0157 !Ferguson base pair geom.
HO 0.0000 0.0000 OPLS Jorgensen, JACS,110,(1988),1657
HS 0.6000 0.0157 W. Cornell CH3SH --> CH3OH FEP
After the MOD4 is specification of vdw parameters. Prior to this you see
the text that is "equivalencing" the vdw parameters of sets of atoms. You
might imagine, for example, that a set of nitrogens has the same vdw, yet
different dihedrals (depending on their connectivity). The text above
says treat NA, N2, N*, NC, NB, NT, NY as equivalent to N. Later in the
nonbond list...
N 1.8240 0.1700 OPLS
N3 1.8240 0.1700 OPLS
NY 1.8240 0.1700 N in nitrile
Technically, NY was already equivalenced (but it also has the same
parameters, so I do not know what trumps what here when it is both
equivalenced but then specified with *different* parameters without more
detailed digging), however all of the other N's equivalenced are not
listed, just "N ". So, the prmtop only contains vdw's for "N " (and not
NA, N2, N*, ...). However the atoms still retain the appropriate type
(for the proper dihedrals. This is why the "printatoms" command shows all
the types.
> Why is the printtype command giving me R* and epsilon parameters? what happened
>
> to missing n and n3?
If you read the manual, printtype prints out the vdw parameters in the
prmtop in the form of R* and epsilon. If you want to see the actual
coefficients (mixed), "printlj". If you want to see the type of each
atom, "printatom"
--tec3
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Received on Tue Aug 03 2010 - 15:00:03 PDT
