[gmx-users] trouble in energy minimization.

Taeho Kim tkim at ifrec.osaka-u.ac.jp
Fri Sep 24 10:45:14 CEST 2010


I used gromacs package (ver 4.0.3) for energy minimization of protein  
homology model.
After em, some residues were mangled if I see structure using jV  
protein structure view (http://www.pdbj.org/jv/index.html) and rasmol.
Especially, some glycine were disappeared on jV viewer and rasmol.

It maybe because that distance between two atoms are far apart, I think.

I used em.mdp and commands for em like below and I attached pdb file  
of mangled region:

cpp = /usr/bin/cpp
define = -DFLEX_SPC
constraints = none
integrator = steep
dt = 0.002
nsteps = 5000
emtol = 1000
emstep = 0.01
nstcomm = 1
ns_type = grid
nstlist = 1
rlist = 1.2
coulombtype = PME
rcoulomb = 1.2
rvdw = 1.2
pbc = xyz

$ pdb2gmx -nointer -ff G43a1 -ignh -missing -f min_struct.pdb -p  
min_struct -o min_struct -i min_struct
$ grompp -f min_struct_scaffold_1 -c min_struct -n min_struct -p  
min_struct -o min_struct
$ mdrun -nice 0 -s min_struct -o min_struct -c min_struct_out.pdb -e  
min_struct -g min_struct.log

Taeho Kim (Ph.D) PostDoctoral Researcher
Systems Immunology Laboratory
WPI Immunology Frontier Research Center
Osaka University, Osaka, 565-0871, Japan

email : tkim at ifrec.osaka-u.ac.jp
home: http://www.ifrec.osaka-u.ac.jp
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100924/08352638/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: mangled_region.pdb
Type: application/octet-stream
Size: 9238 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100924/08352638/attachment.obj>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100924/08352638/attachment-0001.html>

More information about the gromacs.org_gmx-users mailing list