[gmx-users] H2 topology
011013021-Jyotsna
011013021 at bioinfo.sastra.edu
Thu Feb 4 11:01:09 CET 2010
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.abraham at anu.edu.au> wrote:
> *This message was transferred with a trial version of
>CommuniGate(r) Pro*
>
>
> ----- Original Message -----
>From: 011013021-Jyotsna <011013021 at bioinfo.sastra.edu>
> Date: Wednesday, February 3, 2010 21:48
> Subject: Re: [gmx-users] H2 topology
> To: Discussion list for GROMACS users
><gmx-users at 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 <spoel at 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.>spoel at xray.bmc.uu.se spoel at gromacs.org
>> http://folding.bmc.uu.se>--
>> >gmx-users mailing list gmx-users at gromacs.org
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