[gmx-users] How to use ambconv package...

[Tomas Kubar]

Hi

> note that the fourth line of numbers has seven digits in amber7/8
> files, but only six in the amber6 files which ambconv was (I think)
> written for. 

Yes! Ambconv doesn't work with amber7/8 prmtop files.

> There is also a bug in ambconv.c -- (thanks to Anton Feenstra for
> pointing this out).

I use ambconv version dated January 10, 2003 and I can't find such a bug 
there. I noticed that Filip uploaded ambconv to the gmx site in 
November, 2002. I'll have a look if there's a difference between these 
two versions. Tomorrow, now I have to catch the bus..

>>I put the script file (filename is a) like 
>>
>>#!/bin/bash
>>
>># common name for file generation
>>
>>ambconv -v \
>>      -at ala.atop \
>>      -gt ala.top \
>>      -rst ala.rst \
>>      -gro ala.gro
>>
>>Too few command line arguments!AMBCONV v1.0
>>AMBER .top               : ala.atop                        
>>GROMACS .top             : ala.top                         
>>AMBER .rst               : ala.rst                         
>>GROMACS .gro             : ala.gro                         
>>Error: AMBER TOP: too few parameters on second line: Success
>>Error: AMBER TOP: too few parameters on third line: Success
>>Error: AMBER TOP: too few parameters on fourth line: Success

My input looks like
ambconv -v \
         -at $MOL.atop \
         -gt $MOL.top \
         -rst $MOL.rst \
         -gro $MOL.gro \
         -pdb $MOL.pdb \
         -common $COMMON \
         -sol tip3p
and it works. So you may be missing the last 3 parameters.

Furthermore, I would like to pint out that it may be necessary to delete 
the second (blank) line in the .gro file produced. (A bug that shouldn't 
be difficult to remove, but.. :-)

tomas