AMBER Archive (2006)

Subject: RE: AMBER: MM-PBSA problem

From: Ray Luo (rluo_at_uci.edu)
Date: Tue Dec 05 2006 - 13:16:32 CST

Have you applied all bugfixes for Amber8? It might be related to bugfix.49.

 

Ray

 

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
vanessa wai
Sent: Sunday, December 03, 2006 5:52 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: MM-PBSA problem

 

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_at_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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
vanessa wai
Sent: Saturday, December 02, 2006 1:08 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: MM-PBSA problem

 

hi. I used Amber 8.

 

Any ideas?

 

Thanks,

Vanessa

 

 

 

 

 

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