Hi all,
I am doing MM/PBSA calculation from using perl scripts. I create 250
snapshots and pbsa calculation are running perfect for complex and receptor.
I checked calculation properly and found that, when it stats calculation
using sander for 1st snapshot of ligand then its causing problem
This is the error in sander_lig.1.out file.
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
trajectory generated by ptraj
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 0
ERROR IN SETPAR() upon atom distribution
-------------------------------------------
sander_lig.in generated by mm_pbsa.pl. Using MM GB have the fallowing
parametres.
------------------------------------------
File generated by mm_pbsa.pl. Using MM GB
&cntrl
ntf = 1, ntb = 0, dielc = 1.0,
idecomp= 0,
igb = 2, saltcon= 0.00,
offset = 0.09,
intdiel= 1.0, extdiel= 80.0,
gbsa = 0, surften= 1.0,
cut = 999.0, nsnb = 99999,
scnb = 2.0, scee = 1.2,
imin = 1, maxcyc = 1, ncyc = 0,
&end
-----------------------------------------------------------------------------------------------------
can anyone please tel me ..whats exactly wrong with parameters ?
I used same input parameters used in perl scripts of MM/PBSA tutorial.
Thanking u
sushil
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Received on Sun May 30 2010 - 11:30:03 PDT
