<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div>First, this isn't a development-related question, so please use gmx-users instead.</div><div id="AppleMailSignature"><br></div><div id="AppleMailSignature">Second, the program tells you quite explicitly what the problems are and how to read up on it and rectify the issue. What happened when you tried to follow those instructions?</div><div id="AppleMailSignature"><br></div><div id="AppleMailSignature">Cheers,</div><div id="AppleMailSignature"><br></div><div id="AppleMailSignature">Erik</div><div id="AppleMailSignature"><br>Erik Lindahl <<a href="mailto:erik.lindahl@scilifelab.se">erik.lindahl@scilifelab.se</a>><div>Professor of Biophysics</div><div>Science for Life Laboratory</div><div>Stockholm University & KTH</div><div>Office (SciLifeLab): +46 8 524 81567</div><div>Cell (Sweden): +46 73 4618050</div><div>Cell (US): +1 267 3078746</div><div><br></div></div><div><br>On 11 Jan 2017, at 14:40, Kulkarni R <<a href="mailto:alumniphysics@hotmail.com">alumniphysics@hotmail.com</a>> wrote:<br><br></div><blockquote type="cite"><div>
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<div>Hi gromacs users,<br>
<br>
<br>
I am using Gromacs version 5.1.1 and em.mdp is <br>
<br>
<br>
<div>#em.mdp<br>
; to test<br>
; grompp -f em.mdp -c test_GMX.gro -p test_GMX.top -o em.tpr -v<br>
; mdrun -v -deffnm em<br>
#Grompp minimization<br>
integrator = steep<br>
nsteps = 500<br>
nstlist = 10<br>
energy-grps = protein LIG<br>
cutoff-scheme = verlet<br>
vdw-type = cut-off<br>
#energy-grps = protein LIG<br>
rvdw = 1.0<br>
coulombtype = pme<br>
rcoulomb = 1.0</div>
<br>
<br>
While executing the following command through cgywin<br>
<br>
GMX grompp -f em.mdp -c complex_GMX.gro -p complex_GMX.top -o em<br>
<br>
<br>
WARNING 1 [file em.mdp, line 16]:<br>
Unknown left-hand '#energy-grps' in parameter file<br>
<br>
<br>
Setting the LD random seed to 2594680474<br>
Generated 861 of the 861 non-bonded parameter combinations<br>
Generating 1-4 interactions: fudge = 0.5<br>
Generated 861 of the 861 1-4 parameter combinations<br>
Excluding 3 bonded neighbours molecule type 'complex'<br>
Excluding 1 bonded neighbours molecule type 'CL-'<br>
Excluding 2 bonded neighbours molecule type 'WAT'<br>
<br>
NOTE 1 [file complex_GMX.top, line 77771]:<br>
System has non-zero total charge: -0.000243<br>
Total charge should normally be an integer. See<br>
<a href="http://www.gromacs.org/Documentation/Floating_Point_Arithmetic">http://www.gromacs.org/Documentation/Floating_Point_Arithmetic</a><br>
for discussion on how close it should be to an integer.<br>
<br>
<br>
Cleaning up constraints and constant bonded interactions with virtual sites<br>
Removing all charge groups because cutoff-scheme=Verlet<br>
Analysing residue names:<br>
There are: 430 Protein residues<br>
There are: 1 Other residues<br>
There are: 38 Ion residues<br>
There are: 19837 Water residues<br>
Analysing Protein...<br>
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...<br>
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...<br>
<br>
-------------------------------------------------------<br>
Program gmx grompp, VERSION 5.1.1<br>
Source code file: /cygdrive/h/gromacs/gromacs-5.1.1/src/gromacs/gmxpreprocess/readir.c, line: 2585<br>
<br>
Fatal error:<br>
Group LIG referenced in the .mdp file was not found in the index file.<br>
Group names must match either [moleculetype] names or custom index group<br>
names, in which case you must supply an index file to the '-n' option<br>
of grompp.<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" class="OWAAutoLink" id="LPlnk74217" previewremoved="true">
http://www.gromacs.org/Documentation/Errors</a><br>
<br>
How to rectify the error <br>
<br>
* Group LIG referenced in the .mdp file was not found in the index file.<br>
<div>Group names must match either [moleculetype] names or custom index group<br>
names, in which case you must supply an index file to the '-n' option<br>
of grompp *<br>
<br>
Thanks,<br>
Kulkarni.R<br>
</div>
<br>
<br>
<br>
</div>
<br>
<p></p>
</div>
</div></blockquote><blockquote type="cite"><div><span>-- </span><br><span>Gromacs Developers mailing list</span><br><span></span><br><span>* Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a> before posting!</span><br><span></span><br><span>* Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a></span><br><span></span><br><span>* For (un)subscribe requests visit</span><br><span><a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers</a> or send a mail to <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.</span></div></blockquote></body></html>