Op 8 feb 2012 om 19:17 heeft "Andrew DeYoung" <[email protected]> het volgende geschreven:
> Hi, > > I am running Gromacs 4.5.5. I am using a colleague's homemade forcefield, > and I am trying to use g_x2top to generate a .top topology file from a .gro > configuration file. This should be possible, because my colleague's > forcefield contains a file to translate atom names into atom types (a .n2t > library file). > > My configuration file is called conf.gro. I run g_x2top using the command: > > g_x2top -f conf.gro -o out.top -ff select > > The program prompts me for a forcefield, and I choose my colleague's > forcefield, which is located in my working directory. g_x2top runs for a > few minutes and ultimately gives this error message: > > ------------------------------------------------------- > Program g_x2top, VERSION 4.5.5 > Source code file: g_x2top.c, line: 206 > > Fatal error: > Could only find a forcefield type for 7147 out of 7216 atoms > ------------------------------------------------------- > > g_x2top also gives me many other error messages of the form (I get 69 such > messages, where 69 is exactly the number of atoms for which g_x2top could > not find a forcefield type): > > "Can not find forcefield for atom X-INDEX with # bonds" > > where X is an atom name, INDEX is that atom's index in conf.gro, and # is > the number of bonds. > > For example, one of these error messages is "Can not find forcefield for > atom B0-6067 with 3 bonds", and I am wondering if you can please give me > advice on this. B0 is indeed an atom name (for boron) and in conf.gro, atom > 6067 is indeed B0. However, my conf.gro is written such that B0 6067 is > surrounded by four fluorine atoms, since the residue is the anion boron > trifluoride (BF4-): > > 287BF4 B0 6067 1.302 2.728 16.210 0.0905 0.7350 -1.6601 > 287BF4 F1 6068 1.237 2.622 16.271 0.3710 -0.9520 0.6277 > 287BF4 F2 6069 1.267 2.739 16.082 0.9097 -0.5184 -0.3121 > 287BF4 F3 6070 1.425 2.712 16.219 0.2955 -0.5337 -0.0541 > 287BF4 F4 6071 1.262 2.846 16.270 0.6101 -0.5227 0.5296 > > where the boron-fluorine bond lengths here are 0.138499 nm, 0.133154 nm, > 0.124362 nm, and 0.13829 nm, respectively. > > My colleague's .n2t file contains the following line (among many others): > > B0 B 1.1504 10.8100 4 F1 0.1390 F2 0.1390 F3 0.1390 F4 0.1390 > > which means, I think, that g_x2top expects each boron atom to be surrounded > by four fluorine atoms with the bond length 0.1390 nm. > > My question is, why does g_x2top think that boron B0-6067 is bonded to only > 3 atoms: "Can not find forcefield for atom B0-6067 with 3 bonds"? Is it > that the B0-F3 bond length (0.124362 nm) in conf.gro is just too far from > the bond length that it expects (0.1390 nm)? Is there any way to get around > this, to tell g_x2top to be more liberal in accepting bonds? (Probably not, > because in http://manual.gromacs.org/current/online/x2top.html I do not see > any options to modify this, and I understand that the atom selection is > primitive.) The problem is, I guess, that the conf.gro that I have is not a > starting configuration; it is from some frame during my colleague's > simulation, when bonds were stretched and compressed, etc. > > Do you have any advice whereby I could still use this non-starting > configuration? > That was a long story. Two things. 1. Please try the - blen option. 2. You could do one top per molecule for one BF4- and then edit the topol to modify the number. > Thanks so much. > > Andrew DeYoung > Carnegie Mellon University > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
