AMBER Archive (2007)

Subject: AMBER: Molsurf error

From: Pankaj R. Daga (pdaga_at_olemiss.edu)
Date: Fri Aug 17 2007 - 12:46:54 CDT

Hi Amber community,

 

I am carrying our MM-PBSA calculation on one protein-ligand system. The
system contains more than 50000 atoms (including water molecules). The
calculations run fine for around 70 trajectories. But ultimately fails with
error message:

 

****************************************************************************
******

 

molsurf.c:1055: is_buried: Assertion 'sarg1>=0.0' failed

 

Memory Allocation Failed.

 

The input file for binding energy calculations is shown below

 

@GENERAL

PREFIX snapshot

PATH ./

COMPLEX 1

RECEPTOR 1

LIGAND 1

COMPT ../1prd_nw.prmtop

RECPT ../apo.prmtop

LIGPT ../prd.prmtop

GC 0

AS 0

DC 0

MM 1

GB 1

PB 1

MS 1

NM 0

@PB

PROC 2

REFE 0

INDI 1.0

EXDI 80.0

SCALE 2

LINIT 1000

PRBRAD 1.4

ISTRNG 0.0

RADIOPT 0

NPOPT 1

CAVITY_SURFTEN 0.0072

CAVITY_OFFSET 0.00

SURFTEN 0.0072

SURFOFF 0.00

@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

 

@PROGRAMS

 

 

Could you please help me to overcome this error?

 

Thank you

 

 

 

===================================================================
If your ship doesn't come in, swim out to it.......Jonathan Winters
===================================================================
Pankaj R. Daga |
Department of Medicinal Chemistry | e-mail: pdaga_at_olemiss.edu
417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638
University of Mississippi | phone: +1-662-915-1853
University, MS, 38677-1848 |
===================================================================

 

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