[gmx-users] After solvation and before adding ions, number of molecules does not agree

Thomas Lipscomb linuxborg2 at yahoo.com
Wed Feb 11 03:43:21 CET 2015

Dear gmx-users,
It has been two days and I did not see my email to gromacs.org_gmx-users at maillist.sys.kth.se posted on the mailing list, so I am sending it again (below) but this time to gmx-users at gromacs.org
I am following the KALP-15 in DPPC tutorial and am failing getting the topol.top file to include the DPPC lipid molecules.  That is causing me to have 1150 fewer atoms in topol.top than I should have, because topol.top does not count the 23 DPPC molecules.
This is a zip file of all of my stuff following the KALP tutorial (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html)It also includes a picture of my progress (Maximin 3 in the DPPC membrane, yes I am using Maximin 3 instead of KALP-15)KALP.zip
I was on this step (yes I have been intentionally calling it model1_solv.gro instead of system_solv.gro as it is in the tutorial):
/usr/local/gromacs/bin/gmx grompp -f ions.mdp -c model1_solv.gro -p topol.top -o ions.tpr
Then I got this error:Fatal error:number of coordinates in coordinate file (model1_solv.gro, 12266)             does not match topology (topol.top, 11116)
So I changed the topol.top from the above zip file from:[ molecules ]; Compound        #molsProtein_chain_A     1SOL              3625
[ molecules ]; Compound        #molsProtein_chain_A     1DPPC              23SOL              3625
Then I got this error:
Fatal error:No such moleculetype DPPC
So then I added this to my modified topol.top:; Include DPPC topology#include "dppc.itp"
Then I got this error:
Fatal error:No such moleculetype DPPC
Rereading this step:Step Two: Modify the Topology
 I see that trying to #include "dppc.itp" is not the right way to go because it has the same precedence as forcefield.itp.
So my guess as to what is wrong is that I messed up the contents of the gromos53a6_lipid.ff folder somehow when I was making them in "Step Two" of the tutorial.
This seems to say that the problem is probably with these two files in the gromos53a6_lipid.ff folder: ffnonbonded.itp and ffbonded.itphttp://comments.gmane.org/gmane.science.biology.gromacs.user/50436

You can find my gromos53a6_lipid.ff folder in the zip fileKALP.zip

I do not know how to fix ffnonbonded.itp and ffbonded.itp manually because I was just following the tutorial's procedure in how to create them.
What is your advice?

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