Re: [AMBER] Negative value of SASA calculated by surf command in cpptraj

From: kurisaki <kurisaki.ncube.human.nagoya-u.ac.jp>
Date: Mon, 13 Jun 2011 11:49:30 +0900

Dear Dr. Rou,

I cannot send e-mail to your address from some reasons.
I attached the files here; CPPTRAJ-input files; the corresponding parameter
file;
single snapshot coordinate; calculated files on our platform.

Parameter file and coordinated file are named as “check.parmtop” and
“checkTrajSnapshot.mdcrd”, respectively.

You will find two cpptraj input files; “surf_test.sh” and
“surf_test_noMLA.sh”.
The former process all molecules and the latter remove ions and small
molecules in cpptraj process.

The calculated results were written down to “checkSurf.txt” and
“checkSurf_noMLA.txt”.
As you thought, fractioned molecules would be associated with negative SASA
values.

Sincerely yours,

                                             Ikuo Kurisaki




-----Original Message-----
From: kurisaki [mailto:kurisaki.ncube.human.nagoya-u.ac.jp]
Sent: Monday, June 13, 2011 11:29 AM
To: 'AMBER Mailing List'
Subject: Re: [AMBER] Negative value of SASA calculated by surf command in
cpptraj

Dear Dr. Roe,

Thank you for your comment on this problem
And I am really grateful to hear kind proposal.

I will send the CPPTRAJ-input files and the corresponding parameter file and
single snapshot coordinate
And calculated files on our platform.

As you thought, fractioned molecules would be associated with negative SASA
values.

Sincerely yours,

                                             Ikuo Kurisaki

PS: I will e-mail the files to your address.



-----Original Message-----
From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
Sent: Monday, June 06, 2011 12:59 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Negative value of SASA calculated by surf command in
cpptraj

Hi,

Without knowing more details about your calculation (what molecule,
what was the input to cpptraj, etc) I can only hazard a guess.
Obviously a negative surface area has no meaning, but remember that
the LCPO surface calculation that cpptraj performs is only a rough
approximation, and as far as I know there's nothing explicit in the
equations to prevent negative surface areas from resulting. If you're
attempting to calculate the surface area of only a fraction of the
molecule (i.e. you're using an atom mask to specify only part of your
solute) and that region is buried it's possible you could get a
negative number.

Of course, there could also be a bug in the code. If you are willing,
could you send me a topology file, cpptraj input, and at least 1
coordinate frame (preferably an Amber restart file or PDB) that
reproduces the negative surface area so I can look into it? Thanks!

-Dan

On Sun, Jun 5, 2011 at 11:30 PM, kurisaki
<kurisaki.ncube.human.nagoya-u.ac.jp> wrote:
> Dear Amber developers,
>
>
>
> Thank you for kind support every time.
>
>
>
> I have a question for using surf command in cpptraj module.
>
> When I used it, negative SASA values were returned for a case.
>
> What do they mean, physically or numerically?
>
>
>
> Sincerely yours,
>
>
>
>                                     Ikuo Kurisaki
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

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Received on Sun Jun 12 2011 - 20:00:03 PDT
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