[gmx-users] Fw: charmm27 in gromacs- grompp error

[Justin Lemkul]

On 6/13/13 12:37 AM, Revthi Sanker wrote:
>
>
>
> Dear all,
> I am using charmm27 forcefield in gromacs for performing all atom simulations (system comprising of DOPC, cholesteryl ester and protein) .I got the itp file for dopc from the lipid book in which they have mentioned #include "charmm27.ff/ffbonded.itp" and  "charmm27.ff/ffnonbonded.itp" to source to these for the parameters of each bond, angle dihedral etc based on the atom types instead of mentioning explicitly each numerical value from the gromacs directory.But it could not read the file and displayed:
>
> Syntax error - File ffbonded.itp, line 2 Last line read: '[ atomtypes ]' Invalid order for directive defaults
>

ffbonded.itp should not be defining atomtypes, thus the directive is out of 
order in some way.

>   When I commented those lines and again ran grompp, it generated the following error:
>    No default Angle types
> No default Ryckaert-Bell. types.
>
> Kindly suggest me in this
>   issue.
>

Something is badly wrong with the files you're using, but based on the limited 
information you have provided, there is nothing anyone can suggest but to refer 
to Chapter 5 of the manual for required topology hierarchy.  Certain directives 
must precede others.

-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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