I have also noticed exactly this. It tends to throw off about one or two datapoints per thousand or so.
Marcus Arieno
On Jun 6, 2013, at 10:36 AM, setyanto md <stwahyudi.md.gmail.com> wrote:
> 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 - 08:30:03 PDT
