Re: [ccp4bb] arp/warp ligand

[Gerrit Langer]

Dear Sangeetha,

what you noticed is a bug that appears under particular circumstances. 
Sorry for your inconvenience. From your logfile excerpt I think that 
this bug has been observed before and been fixed. The next release will 
include the fixed version, however useless this might sound to you now. 
So if you are in urgent need to get the software running now, please 
contact me in a private communication and send me details about your 
case and your computing environment and we will see what we can do.


Greetings from Hamburg,
Gerrit.

[ccp4bb] arp/warp ligand

[Sangeetha Vedula]

Hi all,

I am trying to fit a ligand into density using ARP/wARP 7.0.1 in CCP4 suite
6.0.2 on CCP4interface 1.4.4.2.

I get an error message telling me to look for the error in a
##_warp_ligand_details.log.

_

Running Refmac5 to refine the protein PDB without the search ligand.

 After refmac, R = 0.177 (Rfree = 0.000)


 The difference electron density map has been calculated.


Segmentation fault

QUITTING ... ARP/wARP module stopped with an error message:
MAPREAD_MODE_GRIDMAKER

*** Look for error message in the file:
29_warp_ligand_details.log


#CCP4I TERMINATION STATUS 0 All done
#CCP4I TERMINATION TIME 16 Mar 2009  14:43:30
#CCP4I MESSAGE Task failed

***
* Information from CCP4Interface script
***
 Error during script execution.
***

When I look at the details file, all I see at the end is (no error message):


 ## COORDINATE READING ##

 Reading apo protein ... done.
 Identifying N and O atoms for h-bond investigations ... done.
 Reading clean search ligand(s) ... (PDBfmt)  done

___

The details file ends thus, regardless of whether I read in a library file
for the ligand or not, the library is one generated from ProDRG or from
refmac.

Funnily enough, the program ends the same way even using input files that I
had used previously, with a previous version of ARP/wARP; input files that
worked before.

Help, please!

Thanks a ton!

Sangeetha.