Re: AMBER: MM-PBSA problem

From: vanessa wai <wai.vanessa.gmail.com>
Date: Mon, 4 Dec 2006 09:52:25 +0800

Hi,

The calculation that I'm doing only involves residues (nucleotides) that are
15 Angstrom away from the ligand to speed up the calculation (no NMODE as
well) and its input is as follow:

.PB
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 1.0
LINIT 1500
PRBRAD 1.6
#
RADIOPT 0
#
FOCUS 0
PERFIL 80.0
CHARGE
SIZE
#
SURFTEN 0.005
SURFOFF 0.0
.MM
DIELC 1.0
.GB
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
.MS
PROBE 0.0

Hope you could shed some lights on this problem and thanks in advance for
helping.
Really appreciate it.

Regards,
Vanessa



On 12/2/06, Ray Luo <rluo.uci.edu> wrote:
>
> We need to know more about your calculation
>
>
>
> Can you attach your mm_pbsa.in file?
>
>
>
> Can you also show the free energies for receptor, ligand and complex? How
> do they agree between PB and GB?
>
>
>
> Best,
>
> Ray
>
>
>
> -----Original Message-----
> *From:* owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] *On
> Behalf Of *vanessa wai
> *Sent:* Saturday, December 02, 2006 1:08 AM
> *To:* amber.scripps.edu
> *Subject:* Re: AMBER: MM-PBSA problem
>
>
>
> hi. I used Amber 8.
>
>
>
> Any ideas?
>
>
>
> Thanks,
>
> Vanessa
>
>
>
>
>
>
>
>
>



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Received on Wed Dec 06 2006 - 06:07:20 PST
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