[gmx-users] x2top

[Nuno Azoia]

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

Tel: +351 253 510 280 - Ext: 517 289
Fax: +351 253 510 293

Mobile: +351 965 382 487
E-mail: nazoia at det.uminho.pt