On 2/3/10 10:18 AM, 011013021-Jyotsna wrote:
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 .
Actually for a single molecule you can just do it in a text editor. Set
the first coordinate to 0 and the second to 0.074 nm.
If genbox doesn't insert it could be because there is no space in the box.
Sorry for the lengthy mail.
Thank you ,
Jyotsna
On Wed, 03 Feb 2010 09:30:21 +0100
David van der Spoel <sp...@xray.bmc.uu.se> 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.
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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