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<blockquote type=cite class=cite cite>[ molecules ]<br>
; Compound #mols<br>
Protein
1<br>
SOL
4045<br><br>
I edited it to:<br><br>
[ molecules ]<br>
; Compound #mols<br>
Protein
1<br>
SOL
4037<br>
CL
2</blockquote><br>
Firstly this should be SOL 4043, since you have only removed two water
molecules to be replaced with the chloride. The topology file
contains number of molecules, not number of atoms.<br><br>
<blockquote type=cite class=cite cite>and ran:<br>
#<br>
grompp -v -f lbfgsmin.mdp -c pep1sol1.gro -p pep1sol1.top -o
pep1sol1.tpr<br><br>
This returned a error of<br><br>
Fatal error: No such moleculetype CL<br><br>
I of course tried Cl,<br><br>
Fatal error: No such moleculetype Cl</blockquote><br>
What is the atom/molecule name for chloride with the forcefield that you
are using?<br><br>
<blockquote type=cite class=cite cite>What am I missing? Do I need to
hand edit the rtp file to include definitions for tip4p water? Forgive my
ignorance, I'm just branching out from gromos96 and SPC
water.</blockquote><br>
Hope that helps some (note I haven't used OPLS-AA and TIP4P myself, so
might be off base, but ....)<br><br>
Catch ya,<br>
<x-sigsep><p></x-sigsep>
<b>Dr. Dallas Warren<br>
</b><i>Research Fellow<br>
</i>Department of Pharmaceutical Biology and Pharmacology<br>
Victorian College of Pharmacy, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<font color="#0000FF"><u>dallas.warren@vcp.monash.edu.au<br>
</u></font>+61 3 9903 9083<br>
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