AMBER Archive (2009)

Subject: Re: [AMBER] MM - PBSA problem

From: musa özboyacı (musaozboyaci_at_gmail.com)
Date: Fri Jan 23 2009 - 07:14:05 CST

Dear All,Thank you very much for your suggestions. I tried the way which
Jenk suggested, but it gave me same output ever time I tried. There is no
problem with GB part. For the way that Niel suggested, well I am not allowed
to change the code. But if this is a bug than I could find a way to change
it. The guy who suggested to change the part in the code, actually is not
sure whether it is a safe way or not.

"By changing index 0 of ELRAELE, EPB, PBNONPOL to 0, MM-PBSA would
complete. Can anyone tell me if this was a valid way of solving the
problem or have I misunderstood something. "

One more thing : Is there any one, who really knows what this ELRAELE
parameter stands for?

Best regards,

Musa

2009/1/23 Niel Henriksen <niel.henriksen_at_utah.edu>

> Hi Musa,
>
> >Dear Amber users,
> >I've trying to use mm-pbsa tool of AMBER, and everytime I use I get the
> same
> >error. I tried every possible suggestions in the old mails. However I
> >couldn't fix the problem. I would be very glad if you help me. Here is my
> >output:
>
> >........
> >=>> Calc delta from raw data
> > No data for 0+0 PB ELRAELE 0
>
> If Jenk's suggestion doesn't work, here is another idea.
>
> I think you may be having a problem that has been reported before. I had a
> similar issue and I used the fix described here:
> http://archive.ambermd.org/200806/0357.html
>
> I don't think there has been an "official" response as to whether this fix
> is valid or not, so use at your own risk (I vaguely remember success at
> comparing results from amber9 with amber10).
>
> -niel
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