[gmx-users] CHARMM-GUI to GROMACS

Zhi Yue zhiyue at umaryland.edu
Mon Oct 21 17:14:12 CEST 2013

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.


*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:zhiyue at umaryland.edu, zhiyue at umd.edu

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