[gmx-users] x2top

[Nuno Azoia]

Sorry about that. I realize now that my question is really very stupid. 
If you try to use pdb2gmx you will have a erro message just like "atom 
type not found".

I have this problem, write first and think a little bit more after.

Nuno Azoia wrote:
> 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