[gmx-users] Adding multiple different ligands with acpype

[Justin Lemkul]

On 6/20/17 5:54 AM, Vytautas Rakeviius wrote:
> Hello,
> I try to add multiple and different ligands with acpype and bump into issue "Invalid order for directive atomtypes" discussed before
> (https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2008-July/035223.html)I can comment out other ligands leaving one and then it seems OK.
> I do as said in that discussion:I add:
> #include "ligand1.acpype/ligand1_GMX.itp"
> #include "ligand2.acpype/ligand2_GMX.itp"into topol.top right after:; Include forcefield parameters
> #include "amber99sb-ildn.ff/forcefield.itp"
> And in bottom ([ molecules ]) I add:ligand1    1
> ligand2    1
> Exact error:Fatal error:
> Syntax error - File isofluraneS_GMX.itp, line 3
> Last line read:
> '[ atomtypes ]'
> Invalid order for directive atomtypes
> How I can fix this?
> 

Apparently each of your ligand .itp files declares its own [atomtypes], meaning 
you're trying to declare new [atomtypes] after having declared a previous 
[moleculetype].  This is not allowed - the force field parameters have to all be 
in place before any molecules can be defined.  Group your [atomtypes] into a 
single .itp file, remove them from the individual ligand .itp files, and then

#include "amber99sb-ildn.ff/forcefield.itp"
#include "myatomtypes.itp"
#include "ligand1.itp"
#include "ligand2.itp"

-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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