Re: [gmx-users] Why pdb2gmx could not accept tip4pd as the water model?
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"; 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"; 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"; 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"? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Why pdb2gmx could not accept tip4pd as the water model?
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, 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"<272699...@qq.com>; > > Date: Fri, Jan 11, 2019 00:31 AM > > To: "gromacs.org_gmx-users"; > > > > 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"; > > > > 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 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Why pdb2gmx could not accept tip4pd as the water model?
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"<272699...@qq.com>; Date: Fri, Jan 11, 2019 00:31 AM To: "gromacs.org_gmx-users"; 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"; 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 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] 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"; 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"; 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"? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] 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"; 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"? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Why pdb2gmx could not accept tip4pd as the water model?
On 1/10/19 11:12 AM, ZHANG Cheng wrote: 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"? The water model must appear in watermodels.dat within the force field subdirectory, and the corresponding .itp file must also be in the force field subdirectory, not in $GMXLIB. -Justin -- == 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 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] 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"? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
