On 22/05/18 21:08, David A Case wrote:
> Thanks for the report. I'm only an occasional user of LMOD, but I can
> probably bring in Istvan Kolossvary to help out.
> Are you able to send files that would allow us to (try to) reproduce the
> problem? That is probably a key first step.
> ...thx...dac
Thanks for your reply, that would be great.
I'm enclosing the NAB file I'm using at the end of this message.
However, unfortunately, I cannot provide you with the pdb file. The reasons are that the protein structure is not yet published, and, in addition, the ligand is covered by a non-disclosure agreement
(for the moment). However, it seems like the problem happens regardless of the actual protein and ligand used, so it should be reproducible with other systems as well.
Thanks,
Charo
NAB code follows
// NAB
#include "xmin_opt.h"
#include "lmod_opt.h"
struct xmin_opt xo;
struct lmod_opt lo;
int rnd_seed;
molecule mol;
int natm;
int eig_recalc, ndim_arnoldi;
int lmod_restart, n_best_conf,mc_option;
int n_lmod_steps, nlig, apply_rigdock;
int n_pose_try, random_seed, verbosity, error_flag;
float ene, minim_grms, ene_window, rtemp;
int lig_start[ dynamic ], lig_end[ dynamic ], lig_cent[ dynamic ];
float x[ dynamic ], g[ dynamic ], x_ref[ dynamic ],
conflib[ dynamic ], lmod_traj[ dynamic ];
float tr_min[ dynamic ], tr_max[ dynamic ], rot_min[ dynamic ],
rot_max[ dynamic ];
int i,max_nof_pdb_files;
float glob_min_energy;
float grms;
string fname,sys_command;
point dummy;
if( mytaskid == 0 ) { // set random seed based on clock
rnd_seed = -rseed(); // rseed() returns a negative num
}
mol = getpdb( "AFB5_DAS534_min.pdb" );
readparm( mol, "AFB5_forlmod_mod.prmtop" );
natm = mol.natoms;
allocate x[ 3*natm ]; allocate g[ 3*natm ]; allocate x_ref[ 3*natm ];
setxyz_from_mol( mol, NULL, x );
xmin_opt_init( xo ); // set up defaults
// Initial minimization:
xo.maxiter = 1000;
xo.grms_tol = 0.05;
xo.method = 3;
xo.m_lbfgs = 5;
xo.print_level = 1;
mm_options( "ntpr=1,gb=0,rgbmax=16.0,cut=16.0,diel=R94 " );
mme_init( mol, NULL, "::ZZZ", dummy, NULL ); // fully flexible moleucle
ene = mme( x, g, 0 );
ene = xmin( mme, natm, x, g, ene,grms, xo);
if( mytaskid == 0 ) {
printf( " Unfrozen minimized energy = %12.3lf\n" , ene );
printf( " Gradient RMS = %12.3lf\n" , grms );
printf( " Iter = %12d\n" , xo.iter );
printf( " CPU time = %12.3f\n\n", xo.xmin_time );
}
lmod_opt_init( lo, xo ); // set up defaults
// Conf search:
lo.niter = 10;
lo.nconf = 50;
lo.minim_grms = 0.1;
lo.nmod = 15;
lo.kmod = 5;
lo.nrotran_dof = 0;
lo.energy_window = 150.;
lo.conf_separation_rms = 1.0;
lo.eig_recalc = lo.niter+1;
lo.ndim_arnoldi = 100;
lo.lmod_restart = 10;
lo.n_best_struct = 10;
lo.mc_option = 2;
lo.rtemp = 3.0;
lo.lmod_step_size_min = 2.0;
lo.lmod_step_size_max = 5.0;
lo.nof_lmod_steps = 0;
lo.lmod_relax_grms = 1.0;
lo.nlig = 1;
lo.apply_rigdock = 1;
lo.nof_poses_to_try = 20;
lo.random_seed = rnd_seed;
lo.print_level = 2;
xo.method = 3;
xo.m_lbfgs = 5;
xo.print_level = 0;
allocate conflib[ lo.nconf * 3*natm ];
allocate lmod_traj[ (lo.niter+1) * 3*natm ];
allocate tr_min[ lo.nlig ]; allocate tr_max[ lo.nlig ];
allocate rot_min[ lo.nlig ]; allocate rot_max[lo.nlig ];
allocate lig_start[ lo.nlig ]; allocate lig_end[ lo.nlig ]; allocate lig_cent[ lo.nlig ];
tr_min[1] = 0.1;
tr_max[1] = 3.5;
rot_min[1] = 30.0;
rot_max[1] = 180.0;
lig_start[1] = 8967;
lig_end[1] = 8991;
lig_cent[1] = 0;
setmol_from_xyz( mol, NULL, x ); // load minimized coords into mol
setxyz_from_mol( mol, NULL, x_ref ); // save minimized coords in x_ref
// for tethering specify restrained atoms based on residue serial number, not pdb number
//mm_options( "wcons=100.0,ntpr=99999 " );
//mme_init( mol, NULL, ":1-44,61-213,226-234,250-304,314-332:", x_ref, NULL ); // tethered atoms specified
// the same with frozen atoms
mm_options( "ntpr=99999 " );
//mme_init( mol, ":66-84,333-337,367-372,392-401,427-432,451-456,476-480,568-569:", "::ZZZ", dummy, NULL ); // moving atoms specified
mme_init( mol, ":72-76,338-342,371-376,396-404,431-436,455-460,480-484,569-570:", "::ZZZ", dummy, NULL ); // moving atoms specified
// mme_init( mol, NULL, "::ZZZ", dummy, NULL ); // fully flexible moleucle
mme( x, g, 1 );
glob_min_energy = lmod( natm, x, g, ene,
conflib, lmod_traj, lig_start, lig_end, lig_cent,
tr_min, tr_max, rot_min, rot_max, xo, lo );
if( mytaskid == 0 ) {
printf( " Glob. min. E = %12.3lf kcal/mol\n", glob_min_energy );
printf( " Time in LMOD = %12.3lf CPU sec\n", lo.lmod_time );
printf( " Time in NAB and libs = %12.3lf CPU sec\n", lo.aux_time );
}
xmin_opt_init( xo ); // set up defaults
// Re-minimize structures with no restraints and save them
// freeparm and readprm is required to reset mme_init
freeparm( mol );
readparm( mol, "AFB5_forlmod_mod.prmtop" );
mme_init( mol, NULL, "::ZZZ", dummy, NULL ); // fully flexible moleucle
xo.maxiter = 0; // recompute unfrozen energies
xo.grms_tol = 0.1;
xo.method = 3;
xo.m_lbfgs = 5;
xo.print_level = 0;
//if( mytaskid == 0 ) {
//
// printf( "\n Unfrozen minimized energies:\n" );
//}
mm_options( "ntpr=1" );
max_nof_pdb_files = lo.nconf;
if( max_nof_pdb_files > lo.nconf ) max_nof_pdb_files = lo.nconf;
for( i = 1; i <= max_nof_pdb_files; i = i+1 )
{
setmol_from_xyz( mol, NULL, conflib[ (i-1)*3*natm + 1 ] ); // read i-th conf
setxyz_from_mol( mol, NULL, x ); // load it to x[]
ene = xmin( mme, natm, x, g, ene, grms, xo); // re-minimize
setmol_from_xyz( mol, NULL, x ); // load x[] into mol
//if( mytaskid == 0 ) {
//
// printf( " conf %3d E = %12.3lf (%12.3lf)\n" , i, ene, grms );
//}
fname = sprintf( "AFB5_DAS534_lmod_dock_%04d_%010d.pdb", i, lo.random_seed );
putpdb( fname, mol ); // save conf in pdb file ("-brook" alternative PDB format)
}
// Load the individual pdb files into a single, multi-pdb file
if( mytaskid == 0 ) {
sys_command = sprintf( "touch AFB5_DAS534_lmod_dock_conf_%010d.pdb", lo.random_seed );
system( sys_command );
for( i = 1; i <= max_nof_pdb_files; i = i+1 )
{
sys_command = sprintf( "echo 'MODEL%8d' >> AFB5_DAS534_lmod_dock_conf_%010d.pdb", i, lo.random_seed );
system( sys_command );
sys_command = sprintf( "cat 'AFB5_DAS534_lmod_dock_%04d_%010d.pdb' >> AFB5_DAS534_lmod_dock_conf_%010d.pdb", i, lo.random_seed, lo.random_seed );
system( sys_command );
sys_command = sprintf( "echo 'ENDMDL' >> AFB5_DAS534_lmod_dock_conf_%010d.pdb", lo.random_seed );
system( sys_command );
}
}
// E N D MAIN
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Received on Wed May 23 2018 - 11:00:03 PDT
