# grep -c P popc-solv.gro 1628 What should I do with this number?
Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <[email protected]> To: Shima Arasteh <[email protected]> Cc: Sent: Saturday, October 6, 2012 6:17 PM Subject: Re: [gmx-users] Model of water On 10/6/12 10:45 AM, Shima Arasteh wrote: > Yes, the system is only POPC and water. > > Then it should be very easy to count how many molecules are in the system using grep. Your topology specifies a lot more atoms than the coordinate file has. The number of water molecules appears right, which leaves only the number of POPC as the problem. -Justin > > > Sincerely, > Shima > > > ----- Original Message ----- > From: Justin Lemkul <[email protected]> > To: Shima Arasteh <[email protected]> > Cc: > Sent: Saturday, October 6, 2012 6:07 PM > Subject: Re: [gmx-users] Model of water > > > > On 10/6/12 10:32 AM, Shima Arasteh wrote: >> OK. >> I did as follow as I described, but there is an error: >> 1.editconf -f popc.pdb -o popc-newbox.gro -c -d 1.0 -bt cubic >> 2.genbox -cp popc-newbox.gro -cs spc216.gro -o popc-solv.gro -p topol.top >> >> Then added #include "charmm36.ff/tip3p.itp" to topol.top >> >> 3.grompp -f em.mdp -c popc-solv.gro -p topol.top -o em.tpr >> Fatal error: >> number of coordinates in coordinate file (popc-solv.gro, 74672) >> does not match topology (topol.top, 104936) >> I checked the water molecules of popc-solv.gro by grep command ; >> >> # grep -c HW popc-solv.gro >> 48696 >> >> >> [ molecules ] >> ; Compound #mols >> POPC 238 >> SOL 24348 >> >> >> >> What is the problem? would you please help me? I think the SOL molecule are >> counted twice!! >> > > You're off by a huge amount of atoms, so something is very wrong. The water > molecules do not appear to be the problem. The number of HW/2 is equal to the > number of SOL molecules. Is the system only POPC in water? No protein or any > other components? > > -Justin > -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * 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/Support/Mailing_Lists
