[gmx-users] Ok now what?

The One And Only chappyboy29 at gmail.com
Sun Aug 25 04:19:41 CEST 2013

I've been able to set up everything correctly according to the tutorial I
found on the website. I got the following error when I typed:
grompp -v -f minim.mdp -c 1qlz-solvated.pdb -p 1qlz.top -o

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
checking input for internal consistency...
processing topology...
Generated 141 of the 1176 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 1 [file 1qlz.top, line 7226]:
  System has non-zero total charge: -2.999999
  Total charge should normally be an integer. See
  for discussion on how close it should be to an integer.

processing coordinates...

Program grompp, VERSION 4.6.3
Source code file:
/Users/christinalin/wget-1.14/gromacs-4.6.3/src/kernel/grompp.c, line: 563

Fatal error:
number of coordinates in coordinate file (1qlz-solvated.pdb, 24574)
             does not match topology (1qlz.top, 24672)

I'm stuck.

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