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, <jalem...@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"<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"? > > -- > ================================================== > > 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.