[gmx-users] CHARMM-GUI to GROMACS

Zhi Yue zhiyue at umaryland.edu
Tue Oct 22 00:55:40 CEST 2013

Hi Justin,

Thanks for your advice. I'll try again. Have a wonderful night!



On Mon, Oct 21, 2013 at 6:51 PM, Justin Lemkul <jalemkul at 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 at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
> ==============================**====================
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*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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