Dear amber user/developer,
I am trying to calculate connoly surface area using molsurf command in
cpptraj.
This is my script:
molsurf out molsurf-prot.dat probe 1.4
according to ambertools 12 manual in page 190 about molsurf if no mask
specified it wil calculate fo all-atom.
I have result for the molsurf from that is lite this :
-----
220 14729.9678
221 14575.6926
222 14637.2180
223 14547.6607
224 -1.0000
225 -1.0000
226 14654.5507
227 14634.6111
228 14724.4856
------
I found some result was -1.000, Why it can happened ? it is normal or my
calculation was wrong ?
Another question:
How to calculate for non-polar surface ?
Do we just make mask for non-polar residue ? or we should make a trick like
this
calculate for all-atom then substract with non-polar surface ?
(*usually i used this in vmd script)
Thank you very much
Setyanto
Kimia-ITB
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Received on Thu Jun 06 2013 - 08:00:02 PDT
