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

[ZHANG Cheng]

Thank you Justin and Mark.


Using "-water select" works:


Select the Water Model:
 1: TIP4P-D   TIP 4-point with increased dispersion
 2: None





------------------ Original ------------------
From:  "ZHANG Cheng"<272699575 at qq.com>;
Date:  Fri, Jan 11, 2019 00:51 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?



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.




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"?