[gmx-users] grompp error

Ken Rotondi ksr at chemistry.umass.edu
Fri Oct 14 21:19:48 CEST 2005

Hello All,

Okay, I'm going to scream. I've made up a .gro and .top file for a 
system I'm working on. I e-minimized and equilibrated the system 
successfully. I'm trying to start the run (using the same .top file I 
used in the set-up) and I receive a grompp error:

Program grompp, VERSION 3.3_beta_20050202
Source code file:  grompp.c, line: 427

Fatal error:
number of coordinates in coordinate file (x.gro, 172177)
		does not match topology (x.top, 0)

Also lots of strange chatter in the output, such as:
' for variable ns-type, using 'Grid'
Next time use one of: 'Grid' 'Simple'
There are 10 of these 'warnings' and in each case the variable used is 
one of the available variables.

The big problem is that the end of the .top file, quite clearly the 
[molecules] section shows 1 protein and 56926 SOL

I've checked all the input files in vi, they're all clean text

I became so frustrated I used the .gro file and pdb2gmx to create a new 
.top file. Running grompp with this new .top file results in the same 
error and chatter.

Any suggestions on how to proceed?

Thanks in advance,


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