[gmx-users] sedoheptulose

Mark Abraham Mark.Abraham at anu.edu.au
Wed Nov 19 17:04:29 CET 2008

Bernhard Knapp wrote:
> thanks for the hints but unfortunately i still can not get the molecule 
> running. i tried with both prodrg server and x2top but with limited success:
> in the first case i generate the gro.pdb and .top file via the 
> webinterface [1] of prodrg by pasting my coordinate file into the 
> textbox. then i run the following commands:
> editconf -f sedoheptulose.gro.pdb -o sedoheptulose.cube.pdb -bt cubic -d 2.0
> genbox -cp sedoheptulose.cube.pdb -cs spc216.gro -o 
> sedoheptulose.water.pdb -p sedoheptulose.top -nice 0
> grompp -np 1 -f em.mdp -c sedoheptulose.water.pdb -p sedoheptulose.top 
> -o sedoheptulose.em.tpr
> but in the grompp commands the following error occurs:
> -------------------------------------------------------
> Program grompp, VERSION 3.3.1
> Source code file: topio.c, line: 388
> Fatal error:
> Invalid order for directive moleculetype, file ""sedoheptulose.top"", 
> line 17
> -------------------------------------------------------
> but in line 17 only "[ moleculetype ]" is written?

This error really means what it says - this directive is given at a time 
when it is not valid. You'll need to understand the .top file format, 
which is explained with an example in section 5.7 of the manual. It 
sounds like you should try out some tutorial material to get a handle on 
some of the GROMACS ways of doing things.

> also in the faq i could not find a real guide how to simulate such a 
> molecule ...

Developing a topology for a "new" molecule is not a good starting place 
for a near-beginner with any MD package. You will need to read relevant 
parts of the manual thoroughly.


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