[gmx-users] Re: grompp error
shika
pqah123 at gmail.com
Tue Oct 23 05:15:07 CEST 2012
Okay thanks for the explanation Justin.
But,i would like to ask you guys about the gro file for water.pdb
whereby I got this file from the example of packmol.
When I running this to the minimization part the error occur was :
WARNING 1 [file topol.top, line 30]:
1050 non-matching atom names
atom names from topol.top will be used
atom names from use_1.gro will be ignored
The pdb water looks like this :
HEADER water
COMPND
SOURCE
HETATM 1 H SOL 1 9.626 6.787 12.673
HETATM 2 H SOL 1 9.626 8.420 12.673
HETATM 3 O SOL 1 10.203 7.604 12.673
CONECT 1 3
CONECT 2 3
CONECT 3 1 2
END
is it suitable for to use it where the water model that i shoud use is spc.?
On Tue, Oct 23, 2012 at 8:56 AM, Justin Lemkul [via GROMACS]
<ml-node+s5086n5002316h80 at n6.nabble.com> wrote:
>
>
> On 10/22/12 8:46 PM, Nur Syafiqah Abdul Ghani wrote:
>
>> Dear All,
>>
>> Right now i want to do another simulation which is water and
>> co-solvent,HFIP.
>> I get the small compound file from
>> http://compbio.biosci.uq.edu.au/atb/download.py?molid=6187#files
>> I need to used the all atom one and the force field that i used is
>> gromos96.
>> Right now i'm done packing the HFIP and the water by using packmol and
>> change all the pdb file into gro file.
>> Therefore I want to minimize them by using the command like below:
>>
>> grompp -f em1.mdp -c mixture.gro -p topol.top -o minimize.tpr -v
>>
>> and the error that coming out is :
>>
>> Fatal error:
>> Syntax error - File solvent.itp, line 1
>> Last line read:
>> '[ atoms ]'
>> Invalid order for directive atoms
>>
>>
>> So, I already checked the problem by gedit the solvent.itp.Here is my itp
>> file :
>>
>
> The first part of an .itp file needs to be a [moleculetype] directive that
> names
> the molecule and defines its number of exclusions.
>
>> [ atoms ]
>> ; nr type resnr resid atom cgnr charge mass total_charge
>> 1 CH0 1 hfi C1 1 0.384 12.0110
>> 2 F 1 hfi F1 1 -0.128 18.9984
>> 3 F 1 hfi F2 1 -0.128 18.9984
>> 4 F 1 hfi F3 1 -0.128 18.9984 ; 0.000
>> .............
>> 9 CH0 1 hfi C3 3 0.384 12.0110
>> 10 F 1 hfi F4 3 -0.128 18.9984
>> ..........
>> ; total charge of the molecule: 0.000
>>
>> [ bonds ]
>> ; ai aj funct c0 c1
>> 1 2 2 0.1360 7.2300e+06
>> 1 3 2 0.1360 4.7700e+06
>> ...........
>> 9 11 2 0.1360 4.7700e+06
>> 9 12 2 0.1360 7.2300e+06
>>
>> [ pairs ]
>> ; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp
>> 1 8 1
>> 1 10 1
>> 1 11 1
>> 1 12 1
>> 2 6 1
>> .......
>> 6 8 1
>> 6 10 1
>> 6 11 1
>> .......
>> 7 11 1
>> 7 12 1
>> 8 9 1
>>
>> [ angles ]
>> ; ai aj ak funct angle fc
>> 2 1 3 2 107.60 507.00
>> 2 1 4 2 107.60 507.00
>> 2 1 5 2 111.40 532.00
>> 3 1 4 2 107.60 507.00
>> ......
>> 5 9 10 2 111.40 532.00
>> 5 9 11 2 111.40 532.00
>> 5 9 12 2 109.50 618.00
>> ..........
>> 11 9 12 2 107.60 507.00
>>
>> [ dihedrals ]
>> ; GROMOS improper dihedrals
>> ; ai aj ak al funct angle fc
>>
>> [ dihedrals ]
>> ; ai aj ak al funct ph0 cp mult
>> 2 1 5 9 1 0.00 3.77 3
>> ........
>>
>> [ exclusions ]
>> ; ai aj funct ; GROMOS 1-4 exclusions
>>
>> and the topology file is :
>>
>
> The first thing you need to #include is the parent force field, from which
> bonded and nonbonded parameters are taken.
>
> -Justin
>
>> ; Include topology for solvent
>> #include "solvent.itp"
>> ;
>> ; Include water topology
>> #include "gromos53a6.ff/spc.itp"
>> ;
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ; i funct fcx fcy fcz
>> 1 1 1000 1000 1000
>> #endif
>> ;
>> [ system ]
>> ; Name
>> solvent in water box
>> ;
>> ;
>> [ molecules ]
>> ; Compound #mols
>> hfi .......
>>
>>
>> Is thereany typing error that i seem cant see?
>> I already compare with other problem but seems that I'm lost.
>>
>> Thanks in advance,
>>
>> Best Regards,
>>
>> Nur Syafiqah Abdul Ghani,
>> Theoretical and Computational Chemistry Laboratory,
>> Department of Chemistry,
>> Faculty of Science,
>> Universiti Putra Malaysia,
>> 43400 Serdang,
>> Selangor.
>> 013-7188131
>> alternative email : [hidden email]
>>
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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--
Best Regards,
Nur Syafiqah Abdul Ghani,
Theoretical and Computational Chemistry Laboratory,
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
43400 Serdang,
Selangor.
013-7188131
alternative email : syafiqahabdulghani at gmail.com
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