[gmx-users] Ok now what?
Emanuel.Birru at monash.edu
Sun Aug 25 04:58:39 CEST 2013
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
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...
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.
Program grompp, VERSION 4.6.3
Source code file:
/Users/christinalin/wget-1.14/gromacs-4.6.3/src/kernel/grompp.c, line: 563
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.
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