[gmx-users] spurious dihedral warnings

[Moore, Jonathan (J)]

Berk,

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.


Thanks,
Jonathan

____________________________
Jonathan Moore, Ph.D.
Research and Engineering Sciences - New Products
Core R&D
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


-----Original Message-----
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)
>
>Hello,
>
>I am using gromacs 3.3.
>
>I have a line in my .itp file that looks like this before I actually 
>define
>a different
>"B" state:
>
>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
>different partial
>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 
>values
>
>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 
>and
>warning-free
>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 
>the
>mass of the
>atom in the "B"-state.
>
>In http://www.gromacs.org/pipermail/gmx-users/2006-January/019269.html 
>it
>seems that
>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 
>ignoring
>warnings. Aren't proper dihedrals defined by the atom types involved? How 
>could changing
>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
without notice.

Berk.


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