Re: [AMBER] errors for surf command in cpptraj

From: Daniel Roe <>
Date: Fri, 15 Aug 2014 11:47:39 -0600


On Fri, Aug 15, 2014 at 10:50 AM, Wei Chen <> wrote:
> 1. Do I need to fix the atom orders? The SASA value I obtained is too
> small. If I gave the dataset name explicitly as "surf SA0 :* out outfile",
> I got a reasonable value of SASA. But the strange thing is that the values
> of SASA are the same for all frames. This did not happen for a smaller
> protein containing only one molecule.

Yes. In particular, the molecule information needs to be correct for
the LCPO algorithm to work correctly. The reason is that cpptraj
excludes solvent atoms from the LCPO calculation. If no molecule
information is set up due to a malformed topology, cpptraj does not
know which atoms are solute and which are solvent, and so LCPO
parameters are not correctly set. You need to add a 'fixatomorder'
command before your 'surf' command, e.g.

fixatomorder outprefix reorder

However, the 'surf' command should still trap this error.

> 2. The last error, "[surf] Not all arguments handled: [ :* ]", also
> happened for the small protein. What does the error mean?
> 3. If I use molsurf instead of surf. I got correct SASA, but it still
> complains:"Error: [molsurf] Not all arguments handled: [ :* ]".

I cannot reproduce these errors with the input you provided. It would
help if you could post your entire cpptraj output.


> Could anyone help? Thank you in advance.
> Wei Chen
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Aug 15 2014 - 11:00:02 PDT
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