Hi Amber users,
I was using the XMIN method in NAB package to minimize my
complex(protein+small molecule). The reason I am doing that is I want to
further calculate entropy by using nmode() in NAB.
I was trying to use PB solvent in minimization and below is my input:
======================================================================================
#include "xmin_opt.h"
struct xmin_opt xo;
molecule m;
int natm;
float xyz[dynamic], fret, grad[dynamic];
float energy, grms;
xmin_opt_init(xo);
xo.maxiter = 40000;
xo.grms_tol = 0.0001;
xo.print_level = 1;
xo.method = 2;
xo.ls_maxatmov = 0.15;
m = getpdb("d1_t23_snap1.pdb");
natm = m.natoms;
allocate xyz[3*natm]; allocate grad[3*natm];
readparm(m,"d1_t23_complex_mbondi2.prmtop");
mm_options("cut=999.0, ntpr=1, nsnb=99999, ipb=2, inp=1, radiopt=0,
cavity_surften=0.005420, cavity_offset=0.920000");
mme_init(m, NULL, "::Z", xyz, NULL);
setxyz_from_mol(m,NULL,xyz);
mme(xyz,grad,0);
xmin(mme,natm,xyz,grad,energy,grms,xo);
putxyz("d1_t23_snap1.crd",natm,xyz);
=======================================================================================
And then, below is the .out file I got after successfully compiling the nab
file:
=======================================================================================
Reading parm file (d1_t23_complex_mbondi2.prmtop)
title:
default_name
mm_options: cut=999.0
mm_options: ntpr=1
mm_options: nsnb=99999
mm_options: ipb=2
mm_options: inp=1
mm_options: radiopt=0
mm_options: cavity_surften=0.005420
mm_options: cavity_offset=0.920000
iter Total bad vdW elect nonpolar EPB
frms
PB Warning in pb_read(): the cavity energy should be correlated to the
SASA when inp=1, so use_sav is reset to 0.
PB Warning in pb_read(): sprob=0.557 is optimized for inp=2 and should not
be used with inp=1. It has been reset to 1.4.
ff: 0 -1052.93 3041.05 -335.43 -2712.21 36.00 -1082.35
1.76e+01
Starting L-BFGS minimisation
PB Warning in pb_read(): the cavity energy should be correlated to the
SASA when inp=1, so use_sav is reset to 0.
PB Warning in pb_read(): sprob=0.557 is optimized for inp=2 and should not
be used with inp=1. It has been reset to 1.4.
PB Bomb in pb_init(): Allocation aborted 151 151
151
151 151 151 151 151 151
151 151 151 151 151 151
151 151 151 151 151 151
151 151 151 151 0 151
151 151 0 151
=======================================================================================
The two warning messages, I don't think they are big problems. Seems like
they can still continue. Actually I can specify parameters for sprob in
mm_options() but use_sav is not recognized in mm_options(). Not sure how
can I eliminate this warning.
But anyway, the biggest problem is "PB Bomb in pb_init(): Allocation
aborted". I browsed around it might related to memory issue(?) but I'm not
so sure about that. I also tried to change spacing parameters for grid but
seems that doesn't help either. Can anybody help me with that? Any
suggestion or enlightenment is appreciated. I just want to know the reason
behind it...
Thank you so much!
Best,
Guqin
--
Guqin SHI
The Ohio State University
College of Pharmacy
500 W. 12th Ave.
Columbus, OH, 43210
(614)688-3531
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Received on Fri May 09 2014 - 12:00:02 PDT
