Hi Justin, Thanks for your advice. I'll try again. Have a wonderful night!
Best Shane On Mon, Oct 21, 2013 at 6:51 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/21/13 11:14 AM, Zhi Yue wrote: > >> Dear all, >> >> I built up my protein in lipid bilayer by CHARMM-GUI and now I want to do >> equilibration by GROMACS. I know GROMACS can build the system, but my >> subsequent production run must be conducted by CHARMM. I want to use >> GROMACS to do equilibration cuz it may take long to get it equilibrated. >> Now I get stuck in some problems. >> >> 1) I'm not quite sure about how to make conversion. I searched the archive >> of the forum. Someone recommended I split the pdb generated by CHARMM-GUI >> into different pdb files for protein, lipid, water and ions, and use >> pdb2gmx to convert them to gro files individually. Then combine those gro >> files and made *.top file manually. Someone also suggested I convert >> original pdb directly to gro. Which one is better? >> >> > Whichever one makes sense to you. I prefer a "clean" approach where you > deal with one molecule at a time, but others do it differently. There's > really no need to have pdb2gmx run through all the water, ions, etc. when > really their topologies can easily be handled with simple #include > statements. > > > 2) I tried both protocols. When I checked the robustness of my structure >> by >> grompp, problems came. As CHARMM-GUI uses TIP3P and it would be better to >> use TIPS3P with lipid (we have tested them with CHARMM36 force field), I'm >> not sure how to change water model. Another problem, the most troublesome, >> > > You change the water model by #including the right topology, hence my > approach above. The CHARMM27 distribution that is built into Gromacs uses > tip3p.itp for the "classic" model and tips3p.itp for the CHARMM-specific > model. Our lab recently released a full CHARMM36 force field, with > tip3p.itp containing both models, toggled by using #ifdef blocks. > > > is that all water molecules whose residue ID's after 9999 could not be >> properly designated (say waters 10000TIP to 10009TIP become 1000TIP which >> has 30 atoms). I don't know why it happened. Is there anything wrong with >> my converting logic in question 1)? I mean, I should not convert water or >> ions, should I? >> >> > The residue numbering is irrelevant, and is simply an outcome of PDB > format, which only allows for 5 digits in residue numbers. It has no > implications for the soundness of the topology or the simulation. > > > 3) CHARMM-GUI uses rectangular or hexagonal boxes but they are supported >> by >> GROMACS. I'm wondering whether there is any direct way to match the box >> type in GROMACS. >> >> > Both are supported natively. See manual section 3.2 and figure 3.2. > > -Justin > > -- > ==============================**==================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) 706-7441 > > ==============================**==================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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 gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- *Zhi Yue* Graduate Research Assistant Computer-Aided Drug Design Center School of Pharmacy University of Maryland 20 Penn St, Rm S612 Baltimore, MD 21201 Email:zhi...@umaryland.edu, zhi...@umd.edu -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
