[gmx-users] Why pdb2gmx could not accept tip4pd as the water model?

[Mark Abraham]

Hi,

Yes the value given to pdb2gmx -water is not configurable in this way. I
suggest you use normal tip4p and edit the resulting topol.top file to
specify the include file you really need.

Mark

On Fri., 11 Jan. 2019, 02:55 Justin Lemkul, <jalemkul at vt.edu> wrote:

>
>
> On 1/10/19 11:51 AM, ZHANG Cheng wrote:
> > I think using "-water tip4pd" will always cause errors, without allowing
> me to select the forcefield. I also put the ff directory to my launching
> folder, but still the same problem.
> >
> >
> > Simply using "-water tip4p" will allow me to select the forcefield. But
> I want to use tip4pd, not tip4p.
> >
>
> Turns out you'll have to make the selection interactively or otherwise
> change the pdb2gmx source code to allow for a new water model to be
> selected.
>
> -Justin
>
> >
> >
> > The below is the error message.
> >
> >
> > GROMACS:      gmx pdb2gmx, version 2018.1
> > Executable:   /usr/local/gromacs/bin/gmx
> > Data prefix:  /usr/local/gromacs
> > Working dir:  /home/lanselibai/Cheng/gromacs/20190110_a99SBdisp
> > Command line:
> >    gmx pdb2gmx -f C226S.pdb -o C226S_processed.gro -water tip4pd -inter
> -ignh -merge interactive
> >
> >
> >
> >
> > -------------------------------------------------------
> > Program:     gmx pdb2gmx, version 2018.1
> > Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276)
> > Function:    void gmx::CommandLineParser::parse(int*, char**)
> >
> >
> > Error in user input:
> > Invalid command-line options
> >    In command-line option -water
> >      Invalid value: tip4pd
> >
> >
> >
> >
> >
> >
> >
> > ------------------ Original ------------------
> > From:  "ZHANG Cheng"<272699575 at qq.com>;
> > Date:  Fri, Jan 11, 2019 00:31 AM
> > To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
> >
> > Subject:  Re: Why pdb2gmx could not accept tip4pd as the water model?
> >
> >
> >
> > Thank you Justin.
> >
> >
> > The "watermodels.dat" and "tip4pd.itp" are already in the ff
> subdirectory.
> >
> >
> > The "watermodels.dat" content is:
> > tip4pd   TIP4P-D   TIP 4-point with increased dispersion
> >
> >
> > But "-water tip4pd" still has the error.
> >
> >
> > ------------------ Original ------------------
> > From:  "ZHANG Cheng"<272699575 at qq.com>;
> > Date:  Fri, Jan 11, 2019 00:12 AM
> > To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
> >
> > Subject:  Why pdb2gmx could not accept tip4pd as the water model?
> >
> >
> >
> > I got the a99SB-disp forcefield with tip4pd.itp as the water model.
> >
> >
> > The a99SB-disp.ff file has been copied:
> "/usr/local/gromacs/share/gromacs/top/a99SB-disp.ff"
> > The tip4pd.itp file has also been copied to
> "/usr/local/gromacs/share/gromacs/top"
> >
> >
> > However using "-water tip4pd" in "pdb2gmx" will cause error:
> >
> >
> > Error in user input:
> > Invalid command-line options
> >    In command-line option -water
> >      Invalid value: tip4pd
> >
> >
> >
> > So how can I properly use the tip4pd in "pdb2gmx"?
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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