Dear Mark,
Your suggestions were very helpful .
As per the literature I am following , It is required that
the dummy atom has mass 0 and charge -0.950.Hence , I
created the following itp file with this in mind.
######
; topology for hydrogen.
[ moleculetype ]
;name nrexcl
H2 2
[ atoms ]
; nr type resnr residu atom cgnr
charge mass ; total charge
1 H 1 H2 H1 1 0.475 1.00800 ; 0.00
2 H 1 H2 H2 1 0.475 1.00800 ; 0.00
3 DUM 1 H2 DUM 1 -0.950 0.00000 ; 0.00
[ virtual_sites2 ]
; Site from funct a
3 1 2 1 0.074
[ constraints ]
1 2 2 0.074
######
But during energy minimization I encountered many
problems.
The errors are:
########### error ##########
Ignoring obsolete mdp entry 'cpp'
Back Off! I just backed up em_ion_out.mdp to
./#em_ion_out.mdp.9#
checking input for internal consistency...
processing topology...
Opening library file
/usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 279 of the 1225 non-bonded parameter
combinations
Opening library file
/usr/local/gromacs/share/gromacs/top/spc.itp
Opening library file
/usr/local/gromacs/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Protein_A'
Excluding 3 bonded neighbours molecule type 'Protein_B'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 2 bonded neighbours molecule type 'H2'
processing coordinates...
double-checking input for internal consistency...
Cleaning up constraints and constant bonded interactions
with virtual sites
renumbering atomtypes...
converting bonded parameters...
ERROR 1 [file 2frv_ion.top, line 40]:
atom DUM (Res H2-6) has mass 0
ERROR 2 [file 2frv_ion.top, line 40]:
atom DUM (Res H2-7) has mass 0
-------------------------------------------------------
Program grompp_d, VERSION 4.0
Source code file: grompp.c, line: 940
Fatal error:
There were 2 errors in input file(s)
----------------------------------------------
####### error ########
Is this due to a problem in the .itp file?
Even though i referred to the previous queries made in the
forum , I was not able to get an answer,
Please guide me as to where I have gone wrong .
Thank You,
jyotsna
On Wed, 03 Feb 2010 22:42:09 +1100
Mark Abraham <mark.abra...@anu.edu.au> wrote:
*This message was transferred with a trial version of
CommuniGate(r) Pro*
----- Original Message -----
From: 011013021-Jyotsna <011013...@bioinfo.sastra.edu>
Date: Wednesday, February 3, 2010 21:48
Subject: Re: [gmx-users] H2 topology
To: Discussion list for GROMACS users
<gmx-users@gromacs.org>
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
What about a two-stage process? Do genbox -ci h2.gro
-nmol 100 when there's no water, and then solvate
*afterwards*.
Or, generate solvent, and get a list of 100 random
numbers in the right range, manually delete those water
molecules to create interstices, update your [molecules]
section, then use genconf -ci and equilibrate carefully
to fix the density.
Or, generate solvent for a box somewhat smaller than the
one you want, use editconf -scale to scale the
coordinates up to create interstices, use genconf -ci and
then minimize really gently to fix all the bond lengths,
and equilibrate carefully to fix the density.
Mark
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 <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.>sp...@xray.bmc.uu.se sp...@gromacs.org
http://folding.bmc.uu.se>--
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