[gmx-users] Re: Asking for help about Gromacs

[Anton Feenstra]

Panapat Uawithya wrote:
[...]
> WARNING 1 [file "system.top", line 26]:
>   Too few parameters on line (source file
> toppush.c, line 932)
> WARNING 2 [file "system.top", line 27]:
>   Too few parameters on line (source file
> toppush.c, line 932)
> WARNING 3 [file "system.top", line 28]:
>   Too few parameters on line (source file
> toppush.c, line 932)
> WARNING 4 [file "system.top", line 29]:
>   Too few parameters on line (source file
> toppush.c, line 932)
> WARNING 5 [file "system.top", line 30]:
>   Too few parameters on line (source file
> toppush.c, line 932)
> Excluding 3 bonded neighbours for Protein 1
> Excluding 3 bonded neighbours for DMPC 128
> Cleaning up temporary file grompp0eMXk2
> Fatal error: No such moleculetype SOL
> 
> Grompp could not recognize SOL. I have include
> spc.itp in the .top file as attached to this
> e-mail. What is your suggestion for this?

As you can see below, you forgot the '#' signs that come in front of the 
'ifdef', 'include', 'else' and 'endif' statements for the water topology 
inclusion (the other ones, forcefield, protein and dmpc, are correct).
These are the lines 26-30 that grompp complains about!

> system.top file
[...]
> ; Include water topology
> ifdef FLEX_SPC
> include "flexspc.itp"
> else
> include "spc.itp"
> endif
[...]

P.S., it is usually better to send your questions to the gromacs mailing 
list (gmx-users at gromacs.org, subscribe first at www.gromacs.org). That 
way, more people will read your question, and the chances of a quick 
response will be higher. In any case, I cc this mail to the list, so it 
will also make it into the archive!

-- 
Groetjes,

Anton

* NOTE: New Phone & Fax numbers (below) *

  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
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