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

[Justin Lemkul]

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
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jalemkul at vt.edu | (540) 231-3129
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