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

[david.evans at ulsop.ac.uk]

Seonah,

I've spent a while getting ambconv to work. You need an old format
prmtop file, and
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. 

There is also a bug in ambconv.c -- (thanks to Anton Feenstra for
pointing this out).
- s_atop* atop; */
                                                                     
                                                                     
   
+/* DAE Insert Anton Feenstra's suggestion on memory allocation */
                                                                     
                                                                     
   
+s_atop   satop; /* static */
+s_atop*  atop;  /* pointer */
                                                                     
                                                                     
  +atop = &satop;  /* set atop to point to satop's adress */

If you email me off-list, I can send you an updated version of
ambconv and a how-to, which work reasonably for me. I still do not
get perfect agreement in energies between the two programs, however,
so it would also be useful for me if you could test this :)

Dave Evans
London School of Pharmacy

---- Message from Seonah Kim <kim at qtp.ufl.edu> at 2004-06-16 12:14:43
------
>Hello,
>
>I am a beginner to learn Gromacs...
>
>I am trying to convert Amber parameter file to Gromacs using ambconv
package.
>But I have some problem and I think this is my stupid problem. Would
you tell me 
>how to use ambconv?
>
>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
>
>and then I type
>prompt>./a
>
>I got the following errors.
>
>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
>Error: EOF while reading from AMBER TOP file: Success
>./a: line 10: 14215 Segmentation fault      (core dumped) ambconv -v
-at 
>ala.atop -gt ala.top -rst ala.rst -gro ala.gro
>
>I think I made stupid error when I run the script but I don't know
why.
>Do I need to specify input and output filename when I run script or
something 
>else?
>
>Thank you for your help in advance.
>
>Seonah Kim.
>
>
>
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