[gmx-users] grompp error on nanotube

Yang Ye leafyoung81-group at yahoo.com
Sat Apr 15 07:50:45 CEST 2006

jackyxh at 163.com wrote:
> -------------
> 4. Made a grompp.mdp file by changing a Gromacs tutor "nmr1.mdp"
> --------------
Why use this nmr1.mdp? Do you intend to use LD? You may get example
parameters from other source, e.g. gmxdemo.
There are
EMBO 2004 Shanghai examples.
> 5.run >grompp -f grompp.mdp -c 005.pdb -p 005.top -o topol
> ----------------
> 6 grompp tells the error:
> -------------
> creating statusfile for 1 node...
> WARNING 1 [file grompp.mdp, line unknown]:
> Unknown left-hand 'bd-temp' in parameter file
> WARNING 2 [file grompp.mdp, line unknown]:
> Unknown left-hand 'zero-temp_time' in parameter file
You may look up for these parameters in the manual. Most warnings in
gromacs are very clear for you to do the corrections.
> checking input for internal consistency...
> calling /usr/bin/cpp...
> cpp: too many input files
> cpp exit code: 256
> -I/usr/share/gromacs/top out.top > grompp4YaaUM'
> The '/usr/bin/cpp' command is defined in the .mdp file
> processing topology...
> processing coordinates...
> -------------------------------------------------------
> Program grompp, VERSION 3.3
> Source code file: grompp.c, line: 427
> Fatal error:
> number of coordinates in coordinate file (005005_35_2.pdb, 700)
> does not match topology (out.top, 0)
Your top file looks fine. correct your mdp file first.

Yang Ye

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