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"<272699...@qq.com>;
Date: Fri, Jan 11, 2019 00:51 AM
To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@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"<272699...@qq.com>;
Date: Fri, Jan 11, 2019 00:31 AM
To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@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"<272699...@qq.com>;
Date: Fri, Jan 11, 2019 00:12 AM
To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@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"?
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