Re: [AMBER] Query about the Glucose Parameters

From: Lachele Foley <>
Date: Sat, 25 Nov 2017 00:37:47 -0500

"For preparing frcmod file, I first used the conversion of Gaussian output
into the mol2 file then by the help of parmchk command made frcmod file."'

What did you do with this frcmod file? You mention it but don't say how
you use it.

It really helps if you give full details. For example, Dave had to guess
that maybe using shake will help. It would help if you show us the mdin
files you are using.

And, again, in your example, you built something called GLC and saved
something called GLA. So, again, this cannot be what you actually did. It
is very important to tell us exactly what you are doing. Please copy and
paste the exact commands you used.

BTW, there are no hydrogens with zero vdW parms in GLYCAM06j.dat (except
the HW for TIP3P, which isn't really glycam). We got rid of such terms
because we had observed behavior like what you describe, but not in plain
glucose. With our charge sets, it would happen very, very rarely and only
in very highly charged situations, for example when a carboxylate group was

If you are using charges you made yourself, it is possible that the charges
are out of balance for the force field and that they are causing this

On Fri, Nov 24, 2017 at 5:11 PM, David A Case <>

> On Fri, Nov 24, 2017, Aashish Bhatt wrote:
> >
> > In the 0GA+ROH library,OH-O is not binding in the preparation of topology
> > and coordinate file. but is getting bound in equilibration.
> This looks a lot like the case one can have when there is no Lennard-Jones
> (vdW) term on a H atom, and it can move arbitrarily close to a nearby
> oxygen
> atom. You should check the electrostatic energy at the point around where
> the
> OH-O distance goes almost to zero: does it become very negative?
> If you have not done so, try turning on SHAKE for hydrogens (ntc=2). If
> the
> dagnosis in the above paragraph is correct, that should prevent this from
> happening.
> [I'd like to encourage all Amber users to switch to gaff2, where there are
> no
> longer any hydrogens with zero vdW parameters.]
> ...hope this helps....dac
> _______________________________________________
> AMBER mailing list

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Fri Nov 24 2017 - 22:00:02 PST
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