Just a very silly question: having a pdb file, why don you use pdb2gmx
instead. It will give you a topology file and you can select any force
field, not only those accepted in x2top.
In the x2top man page there is a Known Problem with ffG43a1.n2t.
Once again, maybe this is silly, but I think it will give you what you need.
Nuno
Bernhard Knapp wrote:
Dear Users
I tried to use the x2top function of gromacs 4 on a sugar-molecule.
But the gromacs says that it requests the ffgmx.n2t library which can
not be found in the default directory. I searched in the whole system
but could not find it. Therefore I also searched on an other system
with gromacs 3.3 and copied the file form there to the system with
gromacs 4. Unfortunately it comes up with the next request as below:
-------------------------------------------------------
Program x2top, VERSION 4.0
Source code file: futil.c, line: 527
Fatal error:
Library file ffG43a1.n2t not found in current dir nor in default
directories.
(You can set the directories to search with the GMXLIB path variable)
-------------------------------------------------------
But I could not find this file neigther on the gromacs 4 nor on the
gromacs 3.3 system ...
Where can I get all those n2t files from? Or am I doing something
wrong? My command is simply:
x2top -f sed.pdb -o sed.top -ff select
with forcefield 0:GROMOS96 43a1 force field
if i use 5: OPLS-AA/L it writes
"Generating bonds from distances...
atom 0" to the command line and gets stuck
where sed.pdb contains only
HETATM 1 CAA DRG 1 -8.720 2.440 -1.910 1.00
20.00 C
HETATM 2 OAB DRG 1 -8.220 1.420 -2.790 1.00
20.00 O
HETATM 3 CAC DRG 1 -9.020 0.470 -3.380 1.00
20.00 C
HETATM 4 OAD DRG 1 -8.430 -0.270 -4.170 1.00
20.00 O
HETATM 5 CAF DRG 1 -10.540 0.220 -3.190 1.00
20.00 C
HETATM 6 OAE DRG 1 -11.330 1.410 -3.060 1.00
20.00 O
HETATM 7 CAG DRG 1 -10.840 -0.720 -2.000 1.00
20.00 C
HETATM 8 OAH DRG 1 -10.270 -0.190 -0.800 1.00
20.00 O
HETATM 9 CAI DRG 1 -10.330 -2.150 -2.280 1.00
20.00 C
HETATM 10 OAJ DRG 1 -10.940 -2.650 -3.470 1.00
20.00 O
HETATM 11 CAK DRG 1 -10.620 -3.170 -1.170 1.00
20.00 C
HETATM 12 OAL DRG 1 -11.900 -2.940 -0.570 1.00
20.00 O
HETATM 13 CAM DRG 1 -9.550 -3.150 -0.060 1.00
20.00 C
HETATM 14 OAN DRG 1 -9.840 -4.150 0.920 1.00
20.00 O
Is this a problem of gromacs or am I really missing libraries or is
the input somehow bad?
sincerely
Bernhard
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--
Nuno Gonçalo Azoia Lopes
Laboratório de Investigação em Acabamento
Departamento de Engenharia Têxtil
Universidade do Minho
Campus de Azurém
4800-058 Guimarães
Portugal
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