[gmx-users] Invalid order for directive atomtypes-

[Justin Lemkul]

On 9/4/15 2:30 PM, Atila Petrosian wrote:
> Dear Justin,
>
> Thanks for you quick answer,
>
> I checked the your suggested link.
>
> these new types and their associated parameters must appear before any
> [moleculetype] directive.
>
> In my lig.itp file, [ atomtypes ] appeared before [ moleculetype ]
> directive.
>
> [ atomtypes ]
> ;name  bond_type    mass    charge   ptype          sigma      epsilon
> h1            h1      0.0000  0.0000  A   2.47135e-01  6.56888e-02
> c3            c3      0.0000  0.0000  A   3.39967e-01  4.57730e-01
> ha            ha      0.0000  0.0000  A   2.59964e-01  6.27600e-02
> ca            ca      0.0000  0.0000  A   3.39967e-01  3.59824e-01
> os            os      0.0000  0.0000  A   3.00001e-01  7.11280e-01
> ho            ho      0.0000  0.0000  A   0.00000e+00  0.00000e+00
> hc            hc      0.0000  0.0000  A   2.64953e-01  6.56888e-02
> c              c      0.0000  0.0000  A   3.39967e-01  3.59824e-01
> oh            oh      0.0000  0.0000  A   3.06647e-01  8.80314e-01
> o              o      0.0000  0.0000  A   2.95992e-01  8.78640e-01
>
> [ moleculetype ]
> ; Name            nrexcl
> solute             3
>
> Why I encountered with error?
>

Because [atomtypes] must appear before *any* [moleculetype] can be introduced, 
not just the ones that make use of those types.  Force field-level directives 
can't come after molecule-level directives.  You #included lig.itp after 
introducing a protein [moleculetype].  You can't do that.

-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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