[gmx-users] Question about fatal error of .gro and .top files

[Tomohiro Hayashi]

thanks, David and Kay, Now it works properly.
Tomo
---
Tomohiro Hayashi at TITECH
hayashi at echem.titech.ac.jp
On 2004/09/19, at 23:21, Kay Gottschalk wrote:

> change the mdp file from 'cpp                 =  /lib/cpp' to 'cpp     
>             =  cpp'.
> K.
>
> On Sep 19, 2004, at 5:12 PM, Tomohiro Hayashi wrote:
>
>> Hi Gromacs Users,
>>
>> I've just started using Gromacs ver. 3.2.1 on Mac OS X Panther 
>> (10.3.5). The installation was successful. But now I'm facing one 
>> problem in testing tutorial examples.
>>
>> I always get same problem in following examples (water and speptide) 
>> just as written in the getting started manual:
>>
>> in the case of water
>> -----
>> Fatal error: number of coordinates in coordinate file (conf.gro, 648)
>>              does not match topology (topol.top, 0)
>> -----
>> and in the case of speptide
>> -----
>> Fatal error: number of coordinates in coordinate file (b4em.gro, 2741)
>>              does not match topology (speptide.top, 0)
>> -----
>> The program always says the number of atoms equal to 0 from .top 
>> files, although the number of atoms is indicated in the .top file, as 
>> shown below (topol.top in the case of water)
>> -----
>> #include "ffgmx.itp"
>> #include "spc.itp"
>>
>> [ system ]
>> Pure Water
>>
>> [ molecules ]
>> SOL 216
>> -----
>> Did anyone have the same problem?? I think this is not a difficult 
>> problem.
>>
>> Thanks in advance,
>> Tomo
>
>