[gmx-users] spurious dihedral warnings
Moore, Jonathan (J)
JMoore2 at dow.com
Fri Feb 3 14:27:12 CET 2006
I don't understand this:
> Specifying nucleic_imp_10 twice has no effect,
> as the the definition ends with a comment, so the
> second definition will be hidden in the comment of the first.
What do you mean by "...the definition ends with a comment, so the second
definition will be hidden in the comment of the first"?
Are you saying that something like (an example from my system) " 13 3
4 7 1 gd_17 gd_17" is not an allowed format for specifying the A-
and B-state dihedrals?
If it isn't allowed, then what is the proper way? Must I specify the
parameters explicitly in the .top file instead of using names like gd_17
that refer to the bon.itp file? That would be a pain.
But I've used that type of format (ending the line with the A-state
parameter set name followed by the B-state parameter set name) to specify
the A- and B-states for all of the bonded interactions. There are plenty of
cases where the B-state torsional parameter name is different from A-state
name. There are also plenty of cases where the name is the same. I only
get the warning when both the A- and B-state parameters are "gd_17", not for
any of the other cases when the A- and B-state names are the same.
Jonathan Moore, Ph.D.
Research and Engineering Sciences - New Products
The Dow Chemical Company
1702 Building, Office 4E
Midland, MI 48674 USA
Phone: (989) 636-9765
Fax: (989) 636-4019
E Mail: jmoore2 at dow.com
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Berk Hess
Sent: Friday, February 03, 2006 7:52 AM
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] spurious dihedral warnings
>From: mernst at tricity.wsu.edu
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] spurious dihedral warnings
>Date: Thu, 2 Feb 2006 13:55:34 -0800 (PST)
>I am using gromacs 3.3.
>I have a line in my .itp file that looks like this before I actually
>43 amber99_40 2 8oG N9 43 0.111 14.01
>amber99_40 0.111 14.01
>I can generate a .tpr file with no warnings. However, when I give it a
>charge in the "B" state:
>43 amber99_40 2 8oG N9 43 0.111 14.01
>amber99_40 0.0577 14.01
>Then I get the following warning from grompp:
>WARNING 1 [file "trimer_A.itp", line 942]:
> No default Proper Dih. types for perturbed atoms, using normal
>Line 942 looks like this:
>41 43 44 58 1 nucleic_imp_10
>The warning persists even when I change it to this:
>41 43 44 58 1 nucleic_imp_10 nucleic_imp_10
>Using gmxcheck, the only difference I find between the warning-bearing
>cases is the different partial charge in the "B"-state on atom 43.
>Further, it turns out that I can also trigger the warning by changing
>mass of the
>atom in the "B"-state.
>Jonathan Moore has encountered this problem before, found no fix, and
>decided to just
>ignore the warnings. I will be ignoring them too for now, but I don't like
>warnings. Aren't proper dihedrals defined by the atom types involved? How
>the atom's partial charge or mass result in dihedral misrecognition?
These warnings are not spurious.
The nucleic_imp_10 definition only defined parameters
for the A-state topology.
If the atoms involved in the interaction are identical in
the A and B state grompp assumes the bonded interaction
is also identical (unless you explicitly set different B state parameters).
If one or more of these atoms have any difference in the A and B state, and
you only specify A-state parameters in the dihedral, I think it is
reasonable to issue a warining, as with different atom properties, the user
might have forgotten to add different dihedral parameters.
Specifying nucleic_imp_10 twice has no effect,
as the the definition ends with a comment, so the second definition will be
hidden in the comment of the first.
That said, it might be useful to have a way to avoid
these warnings, but we also need to make sure the user
will not generate unwanted interaction parameters
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