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? 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, 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? 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. Any comment or suggestion will be appreciated. Thanks. Best -- *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
