[gmx-users] Invalid order for directive atomtypes
Daniele Veclani
danieleveclani at gmail.com
Mon Sep 21 14:53:12 CEST 2015
Dear Justin.
Thanks for you quick answer,
I checked the your suggested link.
But I have that both molecules (solvent and solute) introduce new atoms
types.
How can I do??
best regard
D.V.
2015-09-21 14:15 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 9/21/15 8:06 AM, Daniele Veclani wrote:
>
>> Dear Gromacs Useres
>>
>> I'm trying to study a molecule in methanol (I have already studied this
>> molecule in water) with charmm27 force field.
>>
>> I created the file .itp for methanol (solvent):
>>
>> [ atomtypes ]
>> ; name at.num mass charge ptype sigma epsilon
>> CR 6 12.0110 0.0 A 0.387541 0.230120
>> HCMM 1 1.0079 0.0 A 0.235197 0.092048
>> OR 8 15.9994 0.0 A 0.315378 0.636386
>> HOR 1 1.0079 0.0 A 0.040001 0.192464
>>
>>
>> [ pairtypes ]
>> ; i j func sigma1-4 epsilon1-4 ; THESE ARE 1-4
>> INTERACTIONS
>> CR CR 1 0.338541 0.041840
>> CR HCMM 1 0.286869 0.062059
>> CR OR 1 0.326960 0.163176
>> CR HOR 1 0.189271 0.089737
>>
>> [ moleculetype ]
>> ; Name nrexcl
>> SOL 3
>>
>> [ atoms ]
>> ; nr type resnr resid atom cgnr charge mass
>> 1 CR 1 SOL C 1 0.2800 12.0110
>> 2 HCMM 1 SOL H 2 0.0000 1.0079
>> 3 HCMM 1 SOL H1 3 0.0000 1.0079
>> 4 HCMM 1 SOL H2 4 0.0000 1.0079
>> 5 OR 1 SOL O 5 -0.6800 15.9994
>> 6 HOR 1 SOL H3 6 0.4000 1.0079
>>
>> [ bonds ]
>> ; ai aj fu b0 kb, b0 kb
>> 5 6 1 0.09720 469365.3 0.09720 469365.3
>> 5 1 1 0.14180 303937.5 0.14180 303937.5
>> 2 1 1 0.10930 287014.9 0.10930 287014.9
>> 1 4 1 0.10930 287014.9 0.10930 287014.9
>> 1 3 1 0.10930 287014.9 0.10930 287014.9
>>
>> [ pairs ]
>> ; ai aj fu
>> 2 6 1
>> 3 6 1
>> 4 6 1
>>
>> [ angles ]
>> ; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub
>> 2 1 3 1 108.8360 310.74 108.8360 310.74
>> 2 1 4 1 108.8360 310.74 108.8360 310.74
>> 2 1 5 1 108.5770 470.32 108.5770 470.32
>> 3 1 4 1 108.8360 310.74 108.8360 310.74
>> 3 1 5 1 108.5770 470.32 108.5770 470.32
>> 4 1 5 1 108.5770 470.32 108.5770 470.32
>> 1 5 6 1 106.5030 477.55 106.5030 477.55
>>
>> [ dihedrals ]
>> ; ai aj ak al fu phi0 kphi mult phi0 kphi mult
>> 2 1 5 6 9 0.00 1.2468 1 0.00 1.2468 1
>> 2 1 5 6 9 180.00 -0.5774 2 180.00 -0.5774 2
>> 2 1 5 6 9 0.00 0.7238 3 0.00 0.7238 3
>> 3 1 5 6 9 0.00 1.2468 1 0.00 1.2468 1
>> 3 1 5 6 9 180.00 -0.5774 2 180.00 -0.5774 2
>> 3 1 5 6 9 0.00 0.7238 3 0.00 0.7238 3
>> 4 1 5 6 9 0.00 1.2468 1 0.00 1.2468 1
>> 4 1 5 6 9 180.00 -0.5774 2 180.00 -0.5774 2
>> 4 1 5 6 9 0.00 0.7238 3 0.00 0.7238 3
>>
>> [ dihedrals ]
>> ; ai aj ak al fu xi0 kxi xi0 kxi
>> 1 2 5 4 2 0.00 0.0000 0.00 0.0000
>> 1 2 5 3 2 0.00 0.0000 0.00 0.0000
>>
>>
>> #ifdef POSRES_LIGAND
>> [ position_restraints ]
>> ; atom type fx fy fz
>> 1 1 1000 1000 1000
>> 5 1 1000 1000 1000
>> #endif
>>
>>
>> And I included this file in the topology file:
>>
>> #include "charmm27.ff/forcefield.itp"
>>
>> #include "charmm27.ff/nor-antib.itp"
>>
>> #include "charmm27.ff/metanolo.itp"
>>
>> [ system ]
>> ; Name
>> nor
>>
>> [ molecules ]
>> ; Compound #mols
>> SOL 1000
>> nor-antib 1
>>
>> when I run grompp i get this error:
>>
>> Fatal error:
>> Syntax error - File metanolo.itp, line 7
>> Last line read:
>> '[ atomtypes ]'
>> Invalid order for directive atomtypes
>>
>>
>> What am I doing wrong?? (i use gromacs 5.0.4)
>>
>>
> Please search the archive (I answer this question weekly) and/or visit the
> GROMACS Error page, which discusses this situation/error specifically.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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