[gmx-users] Invalid order for directive atomtypes

[Justin Lemkul]

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

==================================================