Dear Amber users,
I am trying to do residue-wise SASA calculation using 'surf' command in
cpptraj. Below is the script I used for the calculation.
*******************************************************************
trajin md3.crd
strip :WAT,:Na+
center :1-293 mass origin
image origin center
surf res25 :25&!.CA,C,O,N,H out SASA.dat
surf res64 :64&!.CA,C,O,N,H out SASA.dat
surf res65 :65&!.CA,C,O,N,H out SASA.dat
surf res68 :68&!.CA,C,O,N,H out SASA.dat
surf res69 :69&!.CA,C,O,N,H out SASA.dat
******************************************************************
But, for few residues, calculated SASA have negative values. Later, I tried
doing residue-wise SASA for a single snapshot, using 'molsurf', 'surf'
methods implemented in cpptraj as well as using NACCESS (
http://www.bioinf.manchester.ac.uk/naccess/) also. For residue 68, 'surf'
gives -9.497, 'molsurf' gives 139.179 and NACCESS gave 0.22. Considering
all these facts, I have few queries about the residue-wise SASA calculation.
1. Why 'surf' calculation showing negative value for SASA? what could be
the meaning of a negative SASA values?
2. Why there is a huge difference between 'surf' and 'molsurf' SASA
outputs? (-9.497 vs 139.179)
3. Which one of these values are trustable?
4. Is there a better way (or any other programs) to calculating
residue-wise SASA over the trajectories?
Waiting for you valuable reply.
Thanks in advance
Regards
Aneesh
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 26 2013 - 03:30:03 PDT
