Hi, Dan,
Thank you for the suggestion. I added fixatomorder before surf, then get
correct SASA. It turns out that the error, "[surf] Not all arguments
handled: [ :* ]", only appears when I use debug option "-debug 2".
But I notice another strange thing. When I use molsurf as follows:
parm prmtop
trajin mdcrd
solvent none
fixatomorder
molsurf :* out sasa.dat
The SASA value of one frame is -1. The values of other frames are normal. I
could not figure out why.
The following is the output:
CPPTRAJ: Trajectory Analysis. V14.09
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
INPUT: Reading Input from file test.in
[parm 3sgj_parseradii.prmtop]
Reading '3sgj_parseradii.prmtop' as Amber Topology
CHAMBER topology: 1: CHARMM 36 *>>>>>>>>CHARMM36
All-Hydrogen Topology File for Proteins <<
[trajin test.mdcrd]
Reading 'test.mdcrd' as Amber Trajectory
[solvent none]
[fixatomorder]
FIXATOMORDER: Will attempt to fix atom ordering when atom numbering
in molecules is non-sequential.
[molsurf :* out sasa.dat]
MOLSURF: [:*] Probe Radius=1.400
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES:
0: '3sgj_parseradii.prmtop', 10112 atoms, 628 res, box: None, 0 mol, 5
frames
INPUT TRAJECTORIES:
0: 'test.mdcrd' is an AMBER trajectory, Parm 3sgj_parseradii.prmtop
(reading 5 of 5)
Coordinate processing will occur on 5 frames.
TIME: Run Initialization took 0.0000 seconds.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM '3sgj_parseradii.prmtop' (2 actions):
0: [fixatomorder]
Detected 2 molecules.
Re-ordered parm: '3sgj_parseradii.prmtop', 10112 atoms, 628 res,
box: None, 2 mol
1: [molsurf :* out sasa.dat]
MOLSURF: Calculating surface area for 10112 atoms.
----- test.mdcrd (1-5, 1) -----
0% 25% 50% reroute(): cusp edge mismatch
75% 100% Complete.
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
>
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Received on Fri Aug 15 2014 - 13:30:02 PDT
