Hi Amber Users:
I have one question and one problem about amber usage:
First one: disulfide bond info
In my protein, there are two disulfide bonds. Below is my minimization
script using XMIN method in NAB:
=====================================================================================
#include "xmin_opt.h"
//receptor
struct xmin_opt xo;
molecule m;
int natm;
float xyz[dynamic], fret, grad[dynamic];
float energy, grms;
xmin_opt_init(xo);
xo.maxiter = 5000;
xo.grms_tol = 0.0001;
xo.print_level = 1;
xo.method = 3;
xo.ls_maxatmov = 0.15;
m = getpdb("../RAW_PDB/d1_receptor/d1_receptor.pdb.1");
natm = m.natoms;
allocate xyz[3*natm]; allocate grad[3*natm];
readparm(m,"d1_mbondi2.prmtop");
mm_options("cut=999.0, ntpr=1, nsnb=99999, diel=C, gb=1, dielc=1.0");
mme_init(m, NULL, "::Z", xyz, NULL);
setxyz_from_mol(m,NULL,xyz);
mme(xyz,grad,0);
//minimization
xmin(mme,natm,xyz,grad,energy,grms,xo);
putxyz("../RAW_PDB/d1_receptor_xmin/d1_receptor.crd.1",natm,xyz);
=====================================================================================
In the pdb file, I didn't conclude any CONECT card to specify disulfide
bond.
In the prmtop file, when I used tleap, I bonded the disulfide bonds in my
protein. So I suppose the disulfide bond info is included. Am I right?
After minimization, I save coordinates by putxyz() because it has higher
level precision and I will use this crd file to do nmode()
So my question is, here, readparm() can assure that my minimization step
takes disulfide bond into account, right?
My second problem is:
Is it common that minimization get stuck at some level of rmsg...?
Here in the script, I set rmsg to 10^-4 and used XMIN method 3.
624 frames out of 2000 got stuck, which means they can never descend below
10^-4.
Then I switch method to XMIN method 2. Doesn't help at all. If method 3
cannot make it, method 2 definitely doesn't have a chance.
Then I set rmsg to 10^-3. Still, 9 frame out of these 624 frames cannot be
minimized to this level (by method 3).
I also tried conjgrad(). Most of frames can only be minimized to 10^-3.
I checked my input pdb file. They are written from MD trajectory by ptraj.
Nothing seems wrong by just looking at the structures. No weird stretch or
clash.
Any suggestions or tips? Is it true that in my case, I just cannot set a
high rmsg? Does it happen too in your cases? Does it have anything to my
disulfide bonds...?
Thank you very much for your time. Any tips or experience will help a lot!
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 Tue May 27 2014 - 09:30:02 PDT
