Greetings. I'm having a lovely time with my old pal grompp, except for the grumpiness after replacing eight water molecules with ions in my system and discovering -- to my astonishment -- the following message:
"Atoms in the .top are not numbered consecutively from 1" Well, this is interesting, seeing as how it's preventing me from advancing, so is garnering all my attention. So I have a look at my topol.top, and I discover the following: ; BEGIN ; Topology for human aldose reductase with NAD+ and inhibitor ; Include force field #include "ffamber99.itp" ; Include protein topology #include "haldr.itp" ; Include inhibitor topology #include "inh1.itp" ; Include NAD+ topology #include "nad.itp" ; Include water topology #include "ffamber_tip3p.itp" #include "my_ions.itp" [ system ] hAldR with inhibitor in water [ molecules ] ;molecule name number AldoseReductase 1 Inhibitor1 1 NAD 1 SOL 27048 ;SOL 27056 Ions 1 ;END Now, the odd thing is, when I comment out references to the Ions molecule and my_ions.itp, and remove the ions from the .gro file, everything works just fine! (Well, it works fine enough.) That's odd because I haven't treated the ion atoms in my_ions.itp any differently than I treated the atoms in Inhibitor1 or in NAD, other than they're after the water. What might be going on here? Frustrated enough to throw things, but not hard enough to spill my beer, Dan Ensign Stanford University -- "Give up learning, and put an end to your troubles." -- Lao Tzu _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
