I have updated the .top file as well after removing all the overlapping lipids from .gro file
On Thu, Jan 14, 2010 at 10:15 AM, <[email protected]> wrote: > Probably you removed lipids from the gro but not from the top (which you > need to do as well). > > Find a lipid atom name that occurs only once per molecule (In non-united > atom lipids I use P8) > > grep P8 my.gro |wc -l > > This will tell you how many lipids should appear in your top file. > > Chris. > > -- original message -- > > Hi All, > > I am running simulation of a system containing Coarse Grained 1SU4 > (Minimized structure) and Coarse Grained DPPC lipid. I used the INFLATEGRO > script to inflate the lipid and removed the overlapping lipids with > proteins > and then running the energy minimization. > > grommp says there are mismatching of atoms in system.top file (which > consists of DPPC, Protein and W) and inflated_bilayer.gro (Which Inflategro > script developed). I don't know why this is happening and why the atoms are > not matching. Also, is there any problem with the atom2cg.awk script which > MARTINI guys provided or they have any other script which converts the > atomic structure of protein to CG protein so that at the time of simulation > the atoms match. > > I am using the grompp command something like this. > > grompp -f em.mdp -c inflated_bilayer.gro -p system.top -maxwarn 10 > > grompp says: atom name 1 in system.top and inflated_bilayer.gro does not > match (NC3-BCQd) > > and it keeps on going until 2116 atoms. > > I dnt know how to fix this. Reply will be appreciable. > > Thanks, > > Sunny > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100114/4df04b2e/attachment.html > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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