[gmx-users] Re: Fatal error: Atomtype F not found
shika
pqah123 at gmail.com
Thu Oct 4 05:41:30 CEST 2012
Thanks for fast reply.I am very new to this and yes I am confused
my itp file is :
; solvent_HFI.gro.top created by rdparm2gmx.pl Sat May 28 10:25:18 MYT 2005
;
;
[ moleculetype ]
; Name nrexcl
solute 3
[ atoms ]
; nr type resnr residue atom cgnr charge
mass typeB chargeB
1 opls_164 1 HFI F 1 -0.234745 19.000000
2 opls_161 1 HFI C 2 0.705532 12.000000
3 opls_164 1 HFI F1 3 -0.205102 19.000000
4 opls_164 1 HFI F2 4 -0.237125 19.000000
5 opls_158 1 HFI C1 5 -0.119035 12.000000
6 opls_078 1 HFI O 6 -0.600958 16.000000
7 opls_079 1 HFI H1 7 0.468121 1.000000
8 opls_140 1 HFI H 8 0.141115 1.000000
9 opls_161 1 HFI C2 9 0.786317 12.000000
10 opls_164 1 HFI F4 10 -0.230854 19.000000
11 opls_164 1 HFI F5 11 -0.266972 19.000000
12 opls_164 1 HFI F3 12 -0.206295 19.000000
[ bonds ]
; ai aj funct
5 8 1
6 7 1
1 2 1
2 3 1
2 4 1
2 5 1
5 6 1
5 9 1
9 10 1
9 11 1
9 12 1
[ pairs ]
; ai aj funct
1 8 1
2 7 1
3 8 1
4 8 1
7 8 1
7 9 1
8 10 1
8 11 1
8 12 1
1 6 1
1 9 1
2 10 1
2 11 1
2 12 1
3 6 1
3 9 1
4 6 1
4 9 1
6 10 1
6 11 1
6 12 1
[ angles ]
; ai aj ak funct
2 5 8 1
5 6 7 1
6 5 8 1
8 5 9 1
1 2 3 1
1 2 4 1
1 2 5 1
2 5 6 1
2 5 9 1
3 2 4 1
3 2 5 1
4 2 5 1
5 9 10 1
5 9 11 1
5 9 12 1
6 5 9 1
10 9 11 1
10 9 12 1
11 9 12 1
[ dihedrals ]
;i j k l func
1 2 5 8 3
2 5 6 7 3
3 2 5 8 3
4 2 5 8 3
7 6 5 8 3
7 6 5 9 3
8 5 9 10 3
8 5 9 11 3
8 5 9 12 3
1 2 5 6 3
1 2 5 9 3
2 5 9 10 3
2 5 9 11 3
2 5 9 12 3
3 2 5 6 3
3 2 5 9 3
4 2 5 6 3
4 2 5 9 3
6 5 9 10 3
6 5 9 11 3
6 5 9 12 3
I would be grateful if you could highlight things that need to be edited.
One more thing,is OPLSAA forcefield suitable for my non standard molecule?
Thanks in advance,
SHika
On Thu, Oct 4, 2012 at 11:23 AM, Justin Lemkul [via GROMACS]
<ml-node+s5086n5001584h88 at n6.nabble.com> wrote:
>
>
> On 10/3/12 10:43 PM, Nur Syafiqah Abdul Ghani wrote:
>
>> Dear Users,
>>
>> Right now i already done for creating the a gro file from antechamber
>> to gromacs format of my molecule which is hexafluoroisopropanol.
>> But when i want to minimize it in vacuum it show atomtype F not found.
>> Im using oplsaa force field and i already change the atom type
>> according to the force field.
>>
>> Below are my files that i need to used for my minimization :
>>
>> PDB file :
>>
>> HETATM 1 opls_164 HFI A 101 -1.433 -1.291 -0.584 1.00
>> -0.219790
>> HETATM 2 opls_161 HFI A 101 -1.274 -0.111 -0.039 1.00
>> 0.600750
>> HETATM 3 opls_164 HFI A 101 -1.331 -0.244 1.257 1.00
>> -0.208510
>> HETATM 4 opls_164 HFI A 101 -2.292 0.639 -0.413 1.00
>> -0.235630
>> HETATM 5 opls_158 HFI A 101 0.013 0.562 -0.520 1.00
>> 0.064010
>> HETATM 6 opls_078 HFI A 101 0.068 1.864 -0.080 1.00
>> -0.549590
>> HETATM 7 opls_079 HFI A 101 -0.560 2.404 -0.527 1.00
>> 0.438940
>> HETATM 8 opls_140 HFI A 101 0.014 0.485 -1.602 1.00
>> 0.103910
>> HETATM 9 opls_161 HFI A 101 1.289 -0.122 -0.036 1.00
>> 0.652070
>> HETATM 10 opls_164 HFI A 101 2.323 0.430 -0.620 1.00
>> -0.216720
>> HETATM 11 opls_164 HFI A 101 1.282 -1.395 -0.353 1.00
>> -0.223970
>> HETATM 12 opls_164 HFI A 101 1.450 -0.022 1.254 1.00
>> -0.205480
>> CONECT 1 2
>> CONECT 2 1 3 4 5
>> CONECT 3 2
>> CONECT 4 2
>> CONECT 5 2 6 7 8
>> CONECT 6 5
>> CONECT 7 5
>> CONECT 8 5 9 10 11
>> CONECT 9 8
>> CONECT 10 8
>> CONECT 11 8 12
>> CONECT 12 11
>> END
>>
>> also the topology ;
>>
>> ; Include forcefield parameters
>> #include "oplsaa.ff/forcefield.itp"
>> ; Include organic solvent
>> #include "hfi.itp"
>> ; Include water topology
>> #include "oplsaa.ff/spc.itp"
>> #ifdef POSRER_WATER
>> ; Position restraint for each water oxygen
>> [position_restraints]
>> ; i funct fcx fcy fcz
>> 1 1 1000 1000 1000
>> #endif
>> [system]
>> ;Name
>> solute
>> [molecules]
>> ;Compound #mols
>> HFI 1
>>
>>
>> gro file;
>>
>> solvent_HFI.gro.gro created by rdparm2gmx.pl Sat May 28 10:25:18 MYT 2005
>> 12
>> 1HFI opls_164 1 0.354 0.142 0.000
>> 1HFI opls_161 2 0.369 0.260 0.055
>> 1HFI opls_164 3 0.364 0.247 0.184
>> 1HFI opls_164 4 0.267 0.335 0.017
>> 1HFI opls_158 5 0.498 0.328 0.006
>> 1HFI opls_078 6 0.503 0.458 0.050
>> 1HFI opls_079 7 0.440 0.512 0.006
>> 1HFI opls_140 8 0.498 0.320 -0.102
>> 1HFI opls_161 9 0.626 0.260 0.055
>> 1HFI opls_164 10 0.729 0.315 -0.004
>> 1HFI opls_164 11 0.625 0.132 0.023
>> 1HFI opls_164 12 0.642 0.270 0.184
>> 0.62525 0.13233 0.02309
>>
>> is there something wrong of my file?
>
> Your .pdb and .gro files call opls_* atom names, which are actually atom
> types.
> Do not confuse the two.
>
>> Why it cant recognize the F atom??
>
> Without seeing the contents of hfi.itp, it's hard to say aside from the
> general
> statement that you're using an atom type that does not exist. I suspect
> you've
> confused atom types and names, given the coordinate files shown.
>
> -Justin
>
> --
> ========================================
>
> 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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