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