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

david.evans at ulsop.ac.uk david.evans at ulsop.ac.uk
Wed Jun 16 18:41:55 CEST 2004


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
>I am a beginner to learn Gromacs...
>I am trying to convert Amber parameter file to Gromacs using ambconv
>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 
># common name for file generation
>ambconv -v \
>       -at ala.atop \
>       -gt ala.top \
>       -rst ala.rst \
>       -gro ala.gro
>and then I type
>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
>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
>Do I need to specify input and output filename when I run script or
>Thank you for your help in advance.
>Seonah Kim.
>gmx-users mailing list
>gmx-users at gromacs.org
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.

-------------- next part --------------
A non-text attachment was scrubbed...
Name: david_evans.vcf
Type: text/directory
Size: 160 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20040616/197191b0/attachment.bin>

More information about the gromacs.org_gmx-users mailing list