[AMBER] errors for surf command in cpptraj

From: Wei Chen <cwbluesky.gmail.com>
Date: Fri, 15 Aug 2014 12:50:07 -0400


I am using AmberTools14. I try to calculate the SASA of a protein (>10,000
atoms) using LCPO. I used "cpptraj -i input-file". The commands in the
input-file are as folows:
parm parmfile
trajin trajfile
surf :* out outfile

The parmfile is converted from charmm format using chamber. There are two
molecules in the parmfile. Each molecule includes a peptide and a glycan.
All glycans are put behind all peptides so that the atom numbering is not
sequential. When I ran the calculation, although the calculation was
completed, I got the following error messages:

Error: Atom 9556 was assigned a lower molecule # than previous atom. This
Error: happen if 1) bond information is incorrect or missing, or 2) if the
Error: atom numbering in molecules is not sequential. If topology did not
Error: originally contain bond info, 1) can potentially be fixed by
Error: increasing the bondsearch cutoff offset (currently 0.200). 2) can
Error: fixed by either using the 'fixatomorder' command, or using
Error: the 'setMolecules' command in parmed.py.
Error: Could not determine molecule information for 3sgj_parseradii.prmtop.
Error: SetSolventInfo: No molecule information.
Error: Could not determine solvent information for 3sgj_parseradii.prmtop.
Error: [surf] Not all arguments handled: [ :* ]

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.
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: [ :* ]".

Could anyone help? Thank you in advance.

Wei Chen
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Received on Fri Aug 15 2014 - 10:00:03 PDT
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