[gmx-users] Vacuum Minimization Problem

[enklnils at fh-bingen.de]

Hello,

I am new to Gromacs. Despite some experience with EM in Gromacs Waterboxes I am
a kind of stuck. Given the structure of a distorted Tryptophane amino acid
molecule the em is not working well. The Trp Atoms of the imidazole group do
not meet their impropper restraints in the starting structure (eg. The
imidazole is twisted). The MD run I use does not relax the molecule in apropper
way. MD terminates (does not converge) and Trp remains twisted. ?!

I used the MDP file from the Tutorial:
;
;	User spoel (236)
;	Wed Nov  3 17:12:44 1993
;	Input file
;
title               =  drg_trp
cpp                 =  cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  steep
dt		    =  0.002
nsteps              =  5000
nstlist		    =  10
ns_type             =  grid
rlist               =  0.9
coulombtype	    =  PME
rcoulomb            =  0.9
rvdw                =  0.9
fourierspacing      =  0.12
fourier_nx 	    =  0
fourier_ny 	    =  0
fourier_nz 	    =  0
pme_order	    =  4
ewald_rtol	    =  1e-5
optimize_fft	    =  yes
;
;	Energy minimizing stuff
;
emtol               =  1000.0
emstep              =  0.01

PDB File (Trp)
ATOM      1  N   TRP   138     -19.214  28.538 -21.898  1.00  0.00
ATOM      2  CA  TRP   138     -20.284  27.979 -21.277  1.00  0.00
ATOM      3  C   TRP   138     -21.226  27.253 -21.189  1.00  0.00
ATOM      4  O   TRP   138     -21.403  26.343 -20.526  1.00  0.00
ATOM      5  CB  TRP   138     -20.680  29.260 -20.707  1.00  0.00
ATOM      6  CG  TRP   138     -20.374  28.989 -19.530  1.00  0.00
ATOM      7  CD1 TRP   138     -19.327  28.776 -19.225  1.00  0.00
ATOM      8  CD2 TRP   138     -21.072  29.134 -18.664  1.00  0.00
ATOM      9  NE1 TRP   138     -19.432  28.569 -18.245  1.00  0.00
ATOM     10  CE2 TRP   138     -20.303  28.816 -17.786  1.00  0.00
ATOM     11  CE3 TRP   138     -22.191  29.559 -18.367  1.00  0.00
ATOM     12  CZ2 TRP   138     -20.619  28.924 -16.574  1.00  0.00
ATOM     13  CZ3 TRP   138     -22.565  29.659 -17.110  1.00  0.00
ATOM     14  CH2 TRP   138     -21.755  29.334 -16.227  1.00  0.00
ATOM     15  H   TRP   138     -19.096  29.480 -21.881  1.00 99.99
ATOM     16  HD1 TRP   138     -18.614  28.450 -19.812  1.00 99.99
ATOM     17  HE1 TRP   138     -18.891  28.284 -17.943  1.00 99.99
ATOM     18  HE3 TRP   138     -22.576  29.732 -18.827  1.00 99.99
ATOM     19  HZ2 TRP   138     -20.183  28.760 -16.154  1.00 99.99
ATOM     20  HZ3 TRP   138     -23.228  29.916 -16.865  1.00 99.99
ATOM     21  HH2 TRP   138     -22.019  29.404 -15.445  1.00 99.99

Shell script

pdb2gmx -f -ff G43b1 trp.pdb -o trp.gro -p trp.top
grompp -f em.mdp -c trp.gro -
p trp.top -o trp.tpr
mdrun_d -s trp.tpr -o trp.trr -c trp.gro
trjconv -f  trp.trr -s trp.tpr -fit translation -o trp_out.pdb

What is your suggestion?

Nils Enkler
University Regensburg, Germany

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