David van der Spoel
spoel at xray.bmc.uu.se
Wed Feb 8 22:56:18 CET 2012
Op 8 feb 2012 om 19:17 heeft "Andrew DeYoung" <adeyoung at andrew.cmu.edu> het volgende geschreven:
> 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
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
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