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--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, and
Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Fri, May 9, 2014 at 11:44 AM, Guqin Shi <shi.293.osu.edu> wrote:
> 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 - 12:30:02 PDT