[gmx-users] Invalid order for directive atomtypes for ligands

[Justin Lemkul]

On 6/28/18 4:19 PM, Qasim Pars wrote:
> Dear users,
>
> I have a protein bound to two different ligands. LIG1.itp and LIG2.itp
> files of both ligands include [ atomtypes ] part. I get "Invalid order for
> directive atomtypes" error while running energy minimization step. Do I
> have to combine [ atomtypes ] parts of both ligands to get rid of this
> error?

Yes. All parameters must be defined before any molecules can be declared.

http://www.gromacs.org/Documentation/Errors?highlight=errors#Invalid_order_for_directive_xxx

-Justin

> Here is top file of the system:
>
> #include "/amber99sb-ildn.ff/forcefield.itp"
> #include "Protein_chain_A.itp"
> #include "Protein_chain_B.itp"
>
> #include "/amber99sb-ildn.ff/tip3p.itp"
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>     1    1       1000       1000       1000
> #endif
>
> #include "/amber99sb-ildn.ff/ions.itp"
>
>
> #include "LIG1.itp"
> #ifdef POSRES
> #include "posre_LIG1.itp"
> #endif
>
> #include "LIG2.itp"
> #ifdef POSRES
> #include "posre_LIG2.itp"
> #endif
>
> [ system ]
> Protein in water
>
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> Protein_chain_B     1
> LIG1                      1
> LIG2                      1
> SOL                16018
>
> Thanks in advance

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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