AMBER Archive (2009)

Subject: Re: [AMBER] Disappearing common atoms in Amber 10 with TI

From: Khavrutskii, Ilja (
Date: Thu Jul 16 2009 - 16:02:10 CDT


I figured out how to get the dummy atoms added and parameters for them. Using parmchk with options like

parmchk -i original.mol2 -f mol2 -o original.frcmod -a Y

To get all the parameters with regular atom types for the original molecule

then changed manually parameter types in the original.mol2 to dummy.mol2
Then run parmchk again

parmchk -i dummy.mol2 -f mol2 -o dummy.frcmod -a Y

That gives you two frcmod files that you can use to create your final dummy.frcmod

Then you can do something like this:

tleap -s -f pentane2butane.leaprc

Where pentane2butane.leaprc is:

source leaprc.ff99SB
source leaprc.gaff

PNT=loadmol2 hpnt.mol2
loadamberparams hpnt.frcmod
loadamberparams hbtn_dummy.frcmod
check PNT

desc PNT.1

set PNT.1.HA3 charge 0.031400
set PNT.1.CA charge -0.092300
set PNT.1.HA1 charge 0.033300
set PNT.1.CB charge -0.079400
set PNT.1.HB2 charge 0.039000
set PNT.1.HB3 charge 0.036100
set PNT.1.CG charge -0.079500
set PNT.1.HG2 charge 0.036200
set PNT.1.HG3 charge 0.038900
set PNT.1.CD charge -0.059000
set PNT.1.HD2 charge 0.032000
set PNT.1.HD3 charge 0.031400
set PNT.1.CE charge 0.000000
set PNT.1.HE2 charge 0.000000
set PNT.1.HE3 charge 0.000000
set PNT.1.HE1 charge 0.000000
set PNT.1.HA2 charge 0.032000

set PNT.1.CE type vc
set PNT.1.HE2 type vh
set PNT.1.HE3 type vh
set PNT.1.HE1 type vh

saveamberparm PNT hbtn.prmtop hbtn.inpcrd
savepdb PNT hbtn.pdb


vc and vh being the new atom types used in the first step, virtual c and h.

I want the vc-vh bonds that are c-h bonds to be SHAKEn, do I need to wory about make that explicit to Amber or would it understand given the Masses of the atoms?

What would be the best way to ensure that vc-vh bonds are SHAKEn?
Thank you,

On 7/16/09 10:09 AM, "" <> wrote:


> I was trying to disappear/decouple a common atom using icfe=1, ifsc=0, and
> scmask, but that does not seem to work as I get zero in the vdW field of
> DV/DL averages. Does the scmask only work with soft core? If so, is there
> a way to set vdW parameters to zero in the input file or if not using
> xleap/tleap? Thanks,

scmask gives the mask of atoms experiencing soft-core potentials, it is
only read when the soft-core module is active (ifsc /= 0). If you do not
want to use the soft-core module (but I would recommend that you do), you
have to use dummy atoms in your end state. There might be an old tutorial
specifying how to do this, but I couldnt locate it.

Basically, you have to introduce a new atom type with zero vdW parameters
in place of whatever atom disappears. Depending on the nature of your
change, this can lead to severe convergence problems and might require
using klambda >=4.


Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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