Hi,
The key message is here (although a bit buried):
On Fri, Aug 15, 2014 at 1:58 PM, Wei Chen <cwbluesky.gmail.com> wrote:
> MOLSURF: Calculating surface area for 10112 atoms.
> ----- test.mdcrd (1-5, 1) -----
> 0% 25% 50% reroute(): cusp edge mismatch
> 75% 100% Complete.
This indicates that the algorithm encountered a discontinuity in the
surface, which can occasionally happen for certain geometries. You
could try slightly adjusting the probe radius (by e.g. ~0.1), set the
probe radius to 0.0 and the offset to 1.4, or better yet if possible
just ignore that frame in your output.
-Dan
>
> Read 5 frames and processed 5 frames.
> TIME: Trajectory processing: 6.6643 s
> TIME: Avg. throughput= 0.7503 frames / second.
>
> ACTION OUTPUT:
>
> DATASETS:
> 1 data set:
> MSURF_00000 "MSURF_00000" (double), size is 5
>
> DATAFILES:
> sasa.dat (Standard Data File): MSURF_00000
> ---------- RUN END ---------------------------------------------------
> TIME: Total execution time: 6.7511 seconds.
> --------------------------------------------------------------------------------
> To cite CPPTRAJ use:
> Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
> Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
> Theory Comput., 2013, 9 (7), pp 3084-3095.
>
>
>
>
> Thank you again.
>
> Wei
>
>
>
> On Fri, Aug 15, 2014 at 1:47 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> On Fri, Aug 15, 2014 at 10:50 AM, Wei Chen <cwbluesky.gmail.com> 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.
>>
>> -Dan
>>
>> >
>> > Could anyone help? Thank you in advance.
>> >
>> > Wei Chen
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Aug 15 2014 - 13:30:04 PDT
