Re: [AMBER] error on atom parameters

From: Jason Swails <>
Date: Wed, 23 Mar 2011 12:03:56 -0700

Typically, the more information you provide the easier it is for us to debug
what's happening (i.e. how you created your files, what force field you
used, what kind of simulation you're running with input files, etc.).

However, this message only arises in one instance in sander. It appears as
though you're trying to do a GBSA MD simulation using gbsa=1. In this case,
the Fe radius used for calculating the SASA is unknown, so it is just using
Carbon's radius in its place. If you want to provide your own radius,
you'll have to modify the sander source code (search for "Using carbon SA"
in $AMBERHOME/src/sander/mdread.f). You will have to add another

else if (atype == 'Fe') then

block in that area to set that radius properly. You can get descriptions of
the pointers (i.e. l170, l175, etc.) in $AMBERHOME/src/sander/locmem.f.

Hope this helps,

On Wed, Mar 23, 2011 at 11:07 AM, John S <> wrote:

> Dear Amber Users ,
> I am using atom type for Fe , after creating a library file and parameter
> files for the same I saved the topology and input coordinate files.
> When I run the minimization I get the following message in my .out file ,
> Using carbon SA parms for atom type
> Can anyone help me on what this implies.
> Thanks
> John
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Wed Mar 23 2011 - 12:30:02 PDT
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