Dear Ray,
Thanks for your prompt reply!
I have patched all the bugfix and have passed the tests in MM/PBSA folder.
But the version of AmberTools is 1.2 rather than 1.4.Will this cause the
fatal error? I noticed that there are lots of discussions about this problem in
our mailing list, it seems that it still hasn't be resolved since two years ago.
Any suggestions are greatly appreciated.
Thanks in advance!
Jacob
----- Original Message ----
From: "Ray Luo, Ph.D." <ray.luo.uci.edu>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Fri, March 4, 2011 12:09:06 AM
Subject: Re: [AMBER] Unresolved problem about MM/PBSA
Seems that no snapshots were processed ... For Amber10, have you patched the
bugfix? Make sure you can pass all the tests in the mmpbsa folder.
Ray
On Thu, Mar 3, 2011 at 8:01 AM, 祥谦 孔 <iconsdkxq.yahoo.com.cn> wrote:
> Dear amber users, Recently, i am trying to compare the binding free
> energy of a ligand with its different mutant receptors by the MM/PBSA module
> in AMBER10.The first step passed without a hitch and i got 200 sets of
> coordinates.However, when i tried to calculate the binding energy with the
> perl script,i couldn't get the statistics.out file as before. I checked the
> log file and found the warning information that i listed below. I searched
> the archive of our mailing list where someone has proposed this problem
> several years ago, but there may still don't have a valid solution for this
> problem. Any suggestions are greatly appreciated! Thanks in
> advance! Jacob Error information form log file :=>> Doing statistics=>>
> Values of global variables TEMP = 300 R = 8.314 gammaP =
> 0.0072 betaP = 0.00 gammaG = 0.0072 betaG = 0.00=>> Reading
> input=>> Reordering files Final
> order: 1. snapshot_com.all.out: - 2. snapshot_rec.all.out: - 3.
> snapshot_lig.all.out: -=>> Reading files Reading snapshot_com.all.out
> WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1WARNING: Missing
> ELRAELE for PB in 0 -> Taken from -1 WARNING: Missing EPB for PB in 0 ->
> Taken from -1 WARNING: Missing VDWNB for MM in 1 -> Taken from 0
> WARNING: Missing VDW14 for MM in 1 -> Taken from 0 WARNING: Missing
> PBNONPOL for PB in 1 -> Taken from 0 WARNING: Missing ELRAELE for PB in 1
> -> Taken from 0 WARNING: Missing PBCAV for PB in 1 -> Taken from 0
> WARNING: Missing EPB for PB in 1 -> Taken from 0 WARNING: Missing SURF
> for MS in 1 -> Taken from 0 ...........=>> Treat special
> parameters=>> Calc missing parameters Processing MM GAS Doing 1 MM
> ELE No values for MM_ELE existing -> Skipping
>
>
>
>
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Received on Thu Mar 03 2011 - 17:30:04 PST
