[gmx-users] PROBLEM WITH GROMOS96ff

[Justin Lemkul]

On 10/23/15 7:17 AM, Chiara Bello wrote:
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> Dear Gromacs Users,
> I'm doing a simulation of a ligand using GROMOS96 54a7 force field with the 4.6.5 VERSION.
> I added the residue to the .rtp file and to residuetypes.dat, after that I run my .gro file on pdb2gmx and subsequently on genbox but they gave me a .top file in which the ga_xx keys are missed only for the angles between alifatic carbon atoms and H atoms.
> This is a problem when I try to add ions using grompp because it gives me the following errors:
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> [...]
> ERROR 88 [file test.top, line 620]:
>    No default G96Angle types
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> ERROR 89 [file test.top, line 630]:
>    No default Proper Dih. types
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> ERROR 90 [file test.top, line 631]:
>    No default Proper Dih. types
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> ERROR 91 [file test.top, line 635]:
>    No default Proper Dih. types
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> ERROR 92 [file test.top, line 638]:
>    No default Proper Dih. types
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> ERROR 93 [file test.top, line 663]:
>    No default Proper Dih. types
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> NOTE 3 [file test.top, line 750]:
>    System has non-zero total charge: 5.350000
>    Total charge should normally be an integer. See
>    http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>    for discussion on how close it should be to an integer.
>

You have a clearly broken topology; such a fractional charge can't exist.

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> There were 3 notes
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> -------------------------------------------------------
> Program grompp, VERSION 4.6.5
> Source code file: /build/buildd/gromacs-4.6.5/src/kernel/grompp.c, line: 1610
>
> Fatal error:
> There were 93 errors in input file(s)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
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> Topology file is presented as follows:
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> [ angles ]
> ;  ai    aj    ak funct            c0            c1            c2            c3
>      2     1     3     2
>      2     1     4     2
>      2     1     5     2
>      3     1     4     2
>      3     1     5     2
>      4     1     5     2
>      1     5     6     2
>      1     5     7     2    ga_15
>      1     5    11     2    ga_15
>      6     5     7     2
>      6     5    11     2
>      7     5    11     2    ga_15
>      5     7     8     2
>      5     7     9     2
>      5     7    10     2
>      8     7     9     2
>      8     7    10     2
>      9     7    10     2
>      5    11    12     2
>      5    11    13     2
>      5    11    14     2    ga_15
>     12    11    13     2
>     12    11    14     2
>     13    11    14     2
>     11    14    15     2    ga_27
>     11    14    19     2    ga_27
>     15    14    19     2    ga_27
>     14    15    16     2    ga_25
>     14    15    17     2    ga_27
>     etc...
>
> Where the first lines match to H - C(sp3) - H and H - C(sp3) - C(sp3) angles.
> I think that angles must be definited in the force field because they are present also in Alanine and other aminoacids. Is this a problem of my protocol or a bug?

GROMOS96 is a united-atom force field, so aliphatic H are not represented 
explicitly.  You're asking the force field to do something that it was 
specifically designed not to do.  You should probably invest some time reading 
about how the force field works before trying to parametrize a new molecule for it.

-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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