Dear Justin I copied all of files in oplsaa.ff folder in my working directory and edited the atomname2type.n2t file as mentioned in before post in my working directory.
I used these command: ] g_x2top –f .pdb –o .top -pbc –ff oplsaa And gromacs get me: opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t There are 23 names to type translations in file oplsaa.ff Generating bonds from distances... atom 44 Can not find forcefield for atom C21-2 with 3 bonds Can not find forcefield for atom C18-5 with 3 bonds Can not find forcefield for atom C16-10 with 3 bonds Can not find forcefield for atom C20-11 with 3 bonds Can not find forcefield for atom C15-17 with 3 bonds Can not find forcefield for atom C12-18 with 3 bonds Can not find forcefield for atom C7-27 with 3 bonds Can not find forcefield for atom C5-28 with 3 bonds Can not find forcefield for atom C3-33 with 3 bonds Can not find forcefield for atom C2-34 with 3 bonds Can not find forcefield for atom C9-40 with 3 bonds Can not find forcefield for atom C10-41 with 3 bonds Program g_x2top, VERSION 4.5.4 Source code file: g_x2top.c, line: 206 Fatal error: Could only find a forcefield type for 32 out of 44 atoms For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ………………………………………………….. I seem can't read atomname2type.n2t file from my working directory. Thanks very much. Afsaneh On Fri, Jul 19, 2013 at 5:58 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/19/13 8:53 AM, afsaneh maleki wrote: > >> Dear Justin >> >> I want a topology for an arbitrary molecule (44 atom) and I use x2top >> program that .n2t file is it’s input. >> >> The .pdb file is as the following: >> >> ATOM 1 O5 TPT 1 -6.131 -0.245 0.000 0.000000 >> >> ATOM 2 C21 TPT 1 -5.041 0.384 0.000 0.000000 >> >> ATOM 3 O6 TPT 1 -5.040 1.814 0.000 0.000000 >> >> ATOM 4 H12 TPT 1 -5.945 2.134 0.000 0.000000 >> >> ATOM 5 C18 TPT 1 -3.708 -0.387 0.000 0.000000 >> >> ATOM 6 C19 TPT 1 -2.374 0.383 0.000 0.000000 >> >> ATOM 7 H10 TPT 1 -2.373 1.453 0.000 0.000000 >> >> …… >> >> I copied oplsaa.ff folder in my working directory >> >> atomname2type.n2t file is as the following: >> >> O opls_267 -0.495284 15.9994 1 C 0.1214 >> >> C opls_470 0.594326 12.0110 3 C 0.1487 O 0.1306 O 0.1214 >> >> O opls_268 -0.560735 15.9994 2 C 0.1306 H 0.0974 >> >> H opls_270 0.417334 1.0079 1 O 0.0974 >> >> C opls_145 0.037549 12.0110 3 C 0.1487 C 0.1387 C 0.1387 >> >> C opls_145 -0.145422 12.0110 3 C 0.1387 H 0.1087 C 0.1395 >> >> H opls_146 0.110842 1.0079 1 C 0.1087 >> >> …… >> >> I used these command: >> >> ] g_x2top –f .pdb –o .top -pbc –ff oplsaa >> >> >> >> But I get: >> >> opening force field file >> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**atomname2type.n2t >> >> There are 23 name to type translations in file oplsaa.ff >> >> Generating bonds from distances... >> >> atom 44 >> >> Can not find forcefield for atom C21-2 with 3 bonds >> >> Can not find forcefield for atom C18-5 with 3 bonds >> >> Can not find forcefield for atom C16-10 with 3 bonds >> >> Can not find forcefield for atom C20-11 with 3 bonds >> >> Can not find forcefield for atom C15-17 with 3 bonds >> >> Can not find forcefield for atom C12-18 with 3 bonds >> >> Can not find forcefield for atom C7-27 with 3 bonds >> >> Can not find forcefield for atom C5-28 with 3 bonds >> >> Can not find forcefield for atom C3-33 with 3 bonds >> >> Can not find forcefield for atom C2-34 with 3 bonds >> >> Can not find forcefield for atom C9-40 with 3 bonds >> >> Can not find forcefield for atom C10-41 with 3 bonds >> >> >> >> Program g_x2top, VERSION 4.5.4 >> >> Source code file: g_x2top.c, line: 206 >> >> >> >> *Fatal error:* >> >> >> Could only find a forcefield type for 32 out of 44 atoms. >> >> >> >> >> >> How to solve my problem. >> >> Why do gromacs open / >> usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**atomname2type.n2t? I >> copyied oplsaa.ff >> folder in my working directory. Also I edited .n2t file in my folder. >> >> > Put the .n2t file in the working directory, not in an oplsaa.ff > subdirectory. > > -Justin > > -- > ==============================**==================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) 706-7441 > > ==============================**==================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? 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