[gmx-users] Membrane error

X.Periole X.Periole at rug.nl
Tue Apr 4 08:22:14 CEST 2006


On Tue, 4 Apr 2006 00:17:25 -0500
  "Kushal Seth" <kushalseth at gmail.com> wrote:
> HI all !
>> I am gettting this error  while doing my simulation... 
>>for the bilayers
>>
>>
>>
>> Back Off! I just backed up emout-nowater.mdp to 
>>./#emout-nowater.mdp.1#
>> checking input for internal consistency...
>> ...ling /usr/bin/cpp
>> : No such file or directory
>> cpp exit code: 32512
>> -I/usr/local/gromacs/share/gromacs/top 
>> mytop-nowater1.top > gromppdriwHo'
>> ' 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 
>>(binaryCR-Ochol-box-largeZ.pdb,
>> 10280)
>>             does not match topology (mytop-nowater1.top, 
>>0)
>>
there is definitely a problem in the definition of your
system in the mytop-nowater1.top ... the systm does not 
see
any atom in there.

XAvier



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