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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Received on Sun Aug 19 2007 - 06:07:43 PDT
