[gmx-users] Problem with OPLS parameters (too few parameters on line)

[Justin Lemkul]

On 4/17/13 4:28 AM, Parul tew wrote:
> Dear GMX users,
>
> I am working on a protein which I want to simulate in a lipid bilayer
> environment (POPC) and want to use OPLS force field for the same. I
> followed the chris neale  directives to make the necessary changes i.e.
> sigma and epsilon, I incorporated the modified atom types of lipids in
> oplsaanb_lipid.itp
> LO    LO    1    15.9994    0    A    0.29599993    0.87869434
>   ;carbonyl O, OPLS"
> LOM    LOM    1    15.9994    0    A    0.29599993    0.87869434
>   ;carboxyl O, OPLS
>
> I also made changes to the [pair types] and appended them in the
> oplsaanb_lipid.itp file
> [ pair types ]
> ; i    j    func    sigma    epsilon
> LO    LO    1    0.29603763    0.10964147
> LO    LOM    1    0.29603763    0.10964147
> LO    opls_116    1    0.306316902    0.094663158
>
> and also changed the OW to opls_116 and removed HW lines.
> Now I want to generate the tpr file using grompp where I had generated a
> topol_popc.top :
> --------------------------------------------------------------------------------------------------
> ; Include chain topologies
> #include "oplsaa_lipid.ff/forcefield.itp"
> #include "popc.itp"
>
> ; Include water topology
> #include "oplsaa_lipid.ff/spc.itp"
>
> ; System specifications
> [ system ]
> 128-Lipid POPC Bilayer
>
> [ molecules ]
> ; molecule name nr.
> POPC 128
> SOL 2460
> ---------------------------------------------------------
> Now when I run the grompp command it gives me following error:
> ERROR 1 [file ffoplsaanb_lipid.itp, line 852]:
>    Invalid directive pair types
>

It's one word, pairtypes.

> WARNING 1 [file ffoplsaanb_lipid.itp, line 854]:
>    Too few parameters on line (source file toppush.c, line 246)

Fix the above problem and the subsequent warnings should go away.  grompp is 
trying to interpret your pairtypes as atomtypes, since "pair types" was an 
unrecognized directive.

-Justin

> -----
> Generated 359128 of the 359128 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 359128 of the 359128 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'POPC'
>
> There were 91 warnings
>
> -------------------------------------------------------
> Program grompp, VERSION 4.5.5
> Source code file: grompp.c, line: 1372
>
> Fatal error:
> There was 1 error in input file(s)
>
>
> I am not able to get where I am going wrong.
> Thanking you,
> Parul
>

-- 
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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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