[gmx-users] Problem in adding *.itp for 2 different ligands in topol .top

[Justin Lemkul]

On 3/18/13 12:47 PM, Parshvika Sharma wrote:
> Dear gromacs users,
>
> I want to run a protein ligand MD in Gromacs 4.6 using CHARMM forcefield.
> My system consists of 2 non-covalently bound ligands (FAD and NADPH) in the
> active site. I generated the topology files (*.itp) of ligands using
> SWISSPARAM. Before running the energy minimization, I added the *.itp file
> for both ligands in topol.top file as mentioned in the gromacs tutorial.
>
> #include "charmm27.ff/forcefield.itp"
> #include "FAD.itp"
> #include "NDP.itp"
>
> But while running GROMPP I am getting this error,
>
> Syntax error - File NDP.itp, line 7
> Last line read:
> '[ atomtypes ]'
> Invalid order for directive atomtypes
>
> It just accepts the first *.itp mentioned in the topol.top, be it FAD.itp
> or NDP.itp and shows this error for the file mentioned next.
>
> I would like to know the correct way to mention *.itp  in topol.top, if we
> have more than 1 ligand.
>

If each .itp file introduces new [atomtypes], you can't simply #include them. 
All [atomtypes] (like any force field-level directive) must be declared before 
any [moleculetype] is declared.  I posted a detailed explanation of this within 
the last few weeks (hint: check the archive, most topics like this have been 
discussed at length many times).

Net effect?  Merge the two [atomtypes] directives before #including any new 
[moleculetype] blocks.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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