On 04/02/10 21:01, 011013021-Jyotsna wrote:
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
That gets you an asymmetric dummy atom, which seems weird. David told
you how to get a symmetric one. The manual also makes that clear.
[ constraints ]
1 2 2 0.074
######
But during energy minimization I encountered many problems.
Strictly EM is done by mdrun. Your inputs to grompp were invalid, so EM
never commences.
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?
Yep. Dummy atoms need mass, or what is the point?
Mark
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>-- >gmx-users mailing list
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