Hi Musa,
It appears that PB parameters in your mmpbsa input needs to be optimized for the complex system you study. Have you tried changing the PB-Grid Scale "SCALE for .PB" from 2 to 2.5 or some other values between 2 and 4. i would initially test mmpbsa for the first extracted coordinate of the complex species to see if it works with the SCALE parameter you would like to try.
cheers,
Jenk
musa özboyacı <musaozboyaci.gmail.com> wrote: Dear Ray,
I am using Amber 10. I created the coordinates files without any problem.
So, I attach the energy input file. Thanks in advance!
Musa
2009/1/22 Ray Luo
> Dear Musa,
>
> Could you be more specific on which distribution of Amber you are using?
> What's your input file?
>
> All the best,
> Ray
>
> ==========================================
> Ray Luo, Ph.D.
> Associate Professor
> Dept Molecular Biology & Biochemistry
> University of California, Irvine, CA 92697
> USPS: PO Box 3900 Email: rluo.uci.edu
> Phones: (949) 824-9528, 9562
> Web: http://rayl0.bio.uci.edu/
> ==========================================
>
>
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf
> Of musa özboyacı
> Sent: Thursday, January 22, 2009 9:07 AM
> To: AMBER.ambermd.org
> Subject: [AMBER] MM - PBSA problem
>
> 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:
>
>
> =>> Values of global variables
> TEMP = 300
> R = 8.314
> gammaP = 0.00542
> betaP = 0.92
> gammaG = 0.0072
> betaG = 0
> =>> Reading input
> =>> Reordering files
> Final order:
> 1. qq2_com.all.out: -
> 2. qq2_rec.all.out: -
> 3. qq2_lig.all.out: -
> =>> Reading files
> Reading qq2_com.all.out
> WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1
> WARNING: Missing ELRAELE for PB in 0 -> Taken from -1
> WARNING: Missing EPB for PB in 0 -> Taken from -1
> WARNING: Missing PBNONPOL for PB in 1 -> Taken from 0
> WARNING: Missing ELRAELE for PB in 1 -> Taken from 0
> WARNING: Missing EPB for PB in 1 -> Taken from 0
> WARNING: Missing PBNONPOL for PB in 2 -> Taken from 1
> ........
> =>> Treat special parameters
> =>> Calc missing parameters
> Processing MM GAS
> Doing 1 MM ELE
> No values for MM_ELE existing -> Skipping
> Processing MM INT
> ........
> =>> Calc delta from raw data
> No data for 0+0 PB ELRAELE 0
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Received on Fri Jan 23 2009 - 01:25:35 PST
