[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>-- 
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