[gmx-users] Ok now what?

[Emanuel Birru]

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of The One And Only
Sent: Sunday, 25 August 2013 12:20 PM
To: forum
Subject: [gmx-users] Ok now what?

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 1qlz-EM-solvated.tpr

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
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  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)

Check your topology file and make sure that the number of atoms are correct. I guess in your topology you have more water "SOL" atoms than in your pdb file, so check that and amend it accordingly. 
As you are very new for this work it is obvious that you will face so many error, are you planning to post all those errors every time you get one :) As Justin suggested, better for you to invest time in learning with someone before doing anything.