[gmx-users] Question about topology construction.

[Justin Lemkul]

On 3/20/14, 10:21 AM, sujithkakkat . wrote:
> Hello,
>
>    I am using gromacs-4.6.5. For the sake of practice,  I made a .itp file
> for carbon dioxide based on the EMP2 model (J.Phys.Chem 1995, 99,
> 12021-12024) .
>
>    The file is self-contained with all parameters including the [default]
> and [atomtypes].
>
>   I tried to do run a simulation on a system containing only CO2 molecules.
> My topology file included only the .itp which I made and no other
> forcefield.itp is included. (Is it ok to do so?)
>
>   When I try to generate .tpr for an energy minimization, I get the error
> "Found a second defaults directive" which the manual says is due to second
> defaults being set in an included topology file.
>
> BUT,   Here I am defining  'default' only once, which is in the .itp file
> for CO2 which I made and no other .itp from any forcefield is included. So
> I am not sure how it is the "second" default  and what is causing the
> error. Is it necessary that the .itp should be included in some forcefield
> directory although it has all the parameters, and then include it into .top
> as a subset of the forcefield?
>
> Please let me know what you think.
>
> Have a look at the .itp I made for CO2 and please let me know if anything
> is seriously wrong.
>
>
>    [ defaults ]
> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
>     1                     3               no                1.0         1.0
>
> [atomtype]
> ; name        mass        charge     ptype    sigma    epsilon
>     CA        12.01100      0.6512       A      0.2757   0.2339
>     CO        15.99940     -0.3256       A      0.3033   0.6695
>
> [moleculetype]
> ; name  nrexcl
>    CO2    1
>
> [atoms]
> ; nr    type    resnr   residue    atom    cgnr   charge    mass
>    1      CA       1      CO2        CA       1     0.6512    12.0110
>    2      OC       1      CO2        OC1      1    -0.3256    15.9994
>    3      OC       1      CO2        OC2      1    -0.3256    15.9994
>
> [constraints]
> ; i   j   funct    doc
>    1   2     1      0.1149
>    1   3     1      0.1149
>
> [exclusions]
> 1    2    3
> 2    1    3
> 3    1    2
>
> [angles]
> ; i   j   k   funct   a0   ak
>    1   2   3     1     180  1236
>

Linear angles may not be stable, just a forewarning.  I think some improvements 
have been made to the code over the years to help fix previous issues.

> #endif

This #endif doesn't match any #ifdef above.

Your .itp file is almost an entire .top, anyway, but if there is an issue, it's 
probably coming from the .top level.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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