Thank you for your reply!
So XMIN is prepared for following entropy calculation.
I performed MMPBSA calculation, too. I used PB method with inp=1. So I just
wanted to make enthalpy and entropy methods consistent...a little bit
paranoid...? I know PB is more costy. I just took out one pdb to play
around... But I never thought that I can't make it work...
I did try xmin with gb(1 and 5). 1 is because nmode can only do second
derivative on gb=1. 5 is because I read from manual that parameters alpha,
beta, and gamma work better to consistent with PB method...
And I cannot turn on gbsa=1, it keeps telling me that it has to use carbon
SA parms for my F atom... Both in MMGBSA and XMIN...
If cannot solve the memory problem, I will use MMPBSA for enthalpy and gb=1
without considering non-polar effect for entropy... I am not sure if that
would affect results a lot...
Sorry I bring more questions now...
2014-05-09 15:19 GMT-04:00 Ray Luo, Ph.D. <ray.luo.uci.edu>:
> Yes, as you pointed out the warning messages are fine … but the bomb
> means that your machine doesn't have enough memory for the job.
>
> Also, are you sure you are minimizing a protein-ligand complex in the
> pb solvent? It's slow. I think gb with ~12 A cutoff is faster.
>
> Ray
> --
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
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>
--
Guqin SHI
The Ohio State University
College of Pharmacy
608 Riffe Building
496 W. 12th Ave.
Columbus, OH, 43210
(614)688-3531
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Received on Fri May 09 2014 - 14:00:03 PDT
