[gmx-users] on the itp file

[Justin Lemkul]

On 5/10/16 9:53 PM, Brett wrote:
> Dear All,
>
> In the on-line protein-ligand md tutorial, related to the drg.itp file, there is
>
>
>
>
>
> "Let's take a look at the [ atoms ] section of our JZ4 topology:
>
> [ atoms ]
> ;   nr      type  resnr resid  atom  cgnr   charge     mass
>      1       CH3     1  JZ4      C4     1    0.000  15.0350
>      2       CH2     1  JZ4     C14     2    0.059  14.0270
>      3       CH2     1  JZ4     C13     2    0.060  14.0270
>      4         C     1  JZ4     C12     2   -0.041  12.0110
>      5       CR1     1  JZ4     C11     2   -0.026  12.0110
>      6        HC     1  JZ4     H11     2    0.006   1.0080
>      7       CR1     1  JZ4      C7     2   -0.026  12.0110
>      8        HC     1  JZ4      H7     2    0.006   1.0080
>      9       CR1     1  JZ4      C8     2   -0.026  12.0110
>     10        HC     1  JZ4      H8     2    0.007   1.0080
>     11       CR1     1  JZ4      C9     2   -0.026  12.0110
>     12        HC     1  JZ4      H9     2    0.007   1.0080
>     13         C     1  JZ4     C10     3    0.137  12.0110
>     14        OA     1  JZ4     OAB     3   -0.172  15.9994
>     15         H     1  JZ4     HAB     3    0.035   1.0080".
>
> May I ask, for the drg.itp file, we only need contain the  [ atoms ] section, all we should contain every sections of the original drg.itp file?
>

A topology needs to be complete.  The purpose in that section of the tutorial is 
to highlight the deficiencies in the charges and charge groups, so that's only 
involving [atoms].

> Secondly, suppose my ligand itp was not got by the traditional gromacs forcefiled, in this situation should we modify the atom types database we got when we originally installed the gromacs to include the atom types specified for the ligand, or we can have the ligand.itp contains a section with the specific ligand atom types information supplied?
>

You can introduce new atom types in a ligand .itp file if you follow the 
required format of the topology.

http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx

"If the directive in question is atomtypes (which is the most common source of 
this error) or any other bonded or nonbonded [*types] directive, typically the 
user is adding some non-standard species (ligand, solvent, etc) that introduces 
new atom types or parameters into the system. As indicated above, these new 
types and parameters must appear before any [moleculetype] directive. The force 
field has to be fully constructed before any molecules can be defined."

-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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