[gmx-users] Topology error

[Mark Abraham]

On 21/11/2011 9:18 PM, archana sonawani wrote:
> Dear Sir/Madam,
>
> For orienting the protein and membrane, I have used the .mdp and 
> following topology file:
> ;
> ;	File 'topol_popc.top' was generated
> ;	By user: jalemkul (502)
> ;	On host:bevany.biochem.vt.edu  <http://bevany.biochem.vt.edu>
> ;	At date: Fri Oct 20 13:26:53 2006
> ;
> ;	This is your topology file
> ;
> ; Include chain topologies
> #include "gromos53a6_lipid.ff/forcefield.itp"
> #include "popc.itp"
>
> ; Include water topology
> #include "gromos53a6_lipid.ff/spc.itp"
>
> ; Include ion topologies
> #include "gromos53a6_lipid.ff/ions.itp"
>
> ; System specifications
> [ system ]
> 60-Lipid POPC Bilayer
>
> [ molecules ]
> ; molecule name nr.
> POPC 60
> SOL 1536
> After running grompp to generate .tpr file I get following error:
>
> Program grompp, VERSION 4.5.4
>
> Source code file: gmxcpp.c, line: 248
>
> Fatal error:
>
> Topology include file "gromos53a6_lipid.ff/forcefield.itp" not found
>
>
> But in the above topology file, if I change the
>
> #include "gromos53a6_lipid.ff/forcefield.itp" line to *;*include 
> "gromos53a6_lipid.ff/forcefield.itp"
>

This file is not optional, so failing to include anything makes further 
problems. You need such a file. You are doing something non-standard, so 
your burden of following directions, and/or understanding how the 
include file and force field mechanism works is a bit higher than normal :-)

Mark

>
> I get following error:
>
>
> Program grompp, VERSION 4.5.4
>
> Source code file: topio.c, line: 653
>
> Fatal error:
>
> Syntax error - File popc.itp, line 1
>
> Last line read:
>
> '[ moleculetype ]'
>
> Invalid order for directive moleculetype
>
>
> Can anyone help me out...Thanks in adv
>
>

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