Dear David,
Thanks for your reply. From your reply, I get the
impression that the bond length of my hydrogen molecule
gets adjusted duing minimization of the whole system (
protien+water+ inserted hydrogen molecule). But the issue
impending is the insertion of the hydrogen molecule itself
into the protein+water box created in previous step. For
insertion/addition of hydrogen molecules I used the
command:
genbox_d -cp 2frv.conf.gro -o 2frv.solv.gro -p 2frv.top
ci h2.gro nmol 100
It reports to me the inability to add any of the
hydrogen molecules, ie it adds 0 molecules out of 100
requested.
###########error########################
Reading molecule configuration
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
Containing 3 atoms in 1 residue
Initialising van der waals distances...
Try 999
Added 0 molecules (out of 100 requested) of H2
Writing generated configuration to 2frv.solv.gro
Back Off! I just backed up 2frv.solv.gro to
./#2frv.solv.gro.1#
PERIPLASMIC HYDROGENASE; PERIPLASMIC HYDROGENASE
Output configuration contains 8340 atoms in 977 residues
Volume : 1299.08 (nm^3)
Density : 143.043 (g/l)
Number of SOL molecules: 186
Processing topology
Removing line #40 'SOL 39308' from topology file
(2frv.top)
####################error end###############
How do i rectify this problem?
I suspect the problem is due to the bond length of the
hydrogen molecule that I created with 1.66A distance ( as
described in my previous post) and the fact that the gap
between the solvent molecules (in my case , water) is not
big enough to accomodate the H2 molecules(as I had used
the pdb of CO2 and replaced each O with an H and C atom
with dummy atom.). So could you please help me figure out
any tool that helps in adjusting the bond length of my
hydrogen molecule in pdb to the desired length of 0.7A.
Or as you said is it possible to minize a single molecule
using md_run program, as I encountered certain problems in
doing so .
Sorry for the lengthy mail.
Thank you ,
Jyotsna
On Wed, 03 Feb 2010 09:30:21 +0100
David van der Spoel <[email protected]> wrote:
*This message was transferred with a trial version of
CommuniGate(r) Pro*
On 2/3/10 7:52 AM, 011013021-Jyotsna wrote:
Dear Justin ,
Thank you very much for your help.
To create a linear H2 molecule with a dummy atom in the
center is
proving to be quite a difficult task.
Hence , I created a pdb file of CO2 using Cerius(2) ,
and replaced the
atoms in the pdb file with 2 H atoms and a dummy
atom.(since CO2 is a
three atom , linear system i.e the two O atoms replaced
by two H atoms
and the C atom by the dummy)
The problem is the bond distance. For CO2 , it is 1.66 A
but I need the
distance for H2 to be only 0.7 A as per the literature I
am following.
By replacing the atoms in the pdb file , there is a
problem regarding
distance since the coordinates of the pdb also point
towards 1.6 A.
I would be very grateful if you could tell me how I can
build a PDB for
H2 with dummy atom with the right distance.
Thank You,
Jyotsna
Doesn't matter if the pdb is wrong initially, you just
do an energy minimization. What is important is (put in
exact bond length):
[ bonds ]
1 2 1 0.74 500000
[ vsites2 ]
3 1 2 1 0.5
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
Fax: +4618511755.
[email protected] [email protected]
http://folding.bmc.uu.se
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