[gmx-users] Re: grompp error
shika
pqah123 at gmail.com
Tue Oct 23 11:16:11 CEST 2012
Dear to me and all the new users for the gromacs,
Luckily ialready found my error..
I need to find the gro file spc216.gro and pack it with my co-solvent
After that i run it in minimization part by using the command
grompp -f em1.mdp -c pacl.gro -p topol.top -o minimize.tpr -v
mdrun -deffnm minimize -v
Need to edit the em1.mdp by using the highest emtol starting from 1000
and decrease it little by little to get the lowest energy.
Regards,
SHika
On Tue, Oct 23, 2012 at 11:14 AM, Nur Syafiqah Abdul Ghani
<pqah123 at gmail.com> wrote:
> 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
--
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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