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!! Thanks in advance. Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <[email protected]> To: Shima Arasteh <[email protected]>; Discussion list for GROMACS users <[email protected]> Cc: Sent: Saturday, October 6, 2012 4:44 PM Subject: Re: [gmx-users] Model of water On 10/6/12 8:59 AM, Shima Arasteh wrote: > > > To use tip3p water model, I copied popc.top and popc.itp in my working > directory. I removed the line of #include tips3p from top file. Also removed > SOL in moleculetypes. > Then I ran genbox : > #genbox -cp popc.gro -cs spc216.gro -o popc-solv.gro -p popc.top > genbox added SOL but there is not any water model including in my top file, > so I added #include "charmm36.ff/tip3p.itp" to top file manually: > > Next, I ran energy minimization. Is my procedure correct? How would I be sure > that " tip3p " is used as water model? > Your approach is correct. genbox will not write topology information (i.e. #include statements) to your topology for you. It adds coordinates to your configuration and updates the [molecules] section, nothing more. It is up to you to tell grompp what parameters to apply to the water molecules. If your topology #includes a TIP3P topology, that's what grompp will use. -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
