[gmx-users] Vacuum Minimization Problem

[David van der Spoel]

enklnils at fh-bingen.de wrote:
> 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?
Try simulated annealing.


> 
> Nils Enkler
> University Regensburg, Germany
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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