pdb2reslib

[emilyada]

Hi,

I am trying to create cyana.lib file from pdb, and using command pdb2reslib -i 11.pdb -o PCys.lib

but I got message like PDB file /11.pdb: Couldn't open.

So how can I create this for untypical amino acid residue from pdb file

[emilyada]

and if I write command as pdb2reslib -i/ PCys.pdb -o/ PCys.lib

I get the message non-option ARGV-elements: PCys.pdb PCys.lib

so how can I make this conversion work?

[yokochi47]

Hi,

Thank you for your comment on pdb2reslib. The command usage shown in the first post is correct.

pdb2reslib -i foo.pdb -o foo.lib

But, The' /11.pdb' message was strange if you specified the file in current directory. Please try absolute path to the PDB as follows:

pdb2reslib -i /home/(path_to_current_dir)/11.pdb

It just prompts result on your terminal by omitting the '-o' argument.

Best regards,

Masashi

[emilyada]

Thanks Masashi, now I get this error:

bash-3.2$ pdb2reslib -i /Users/adaligie/Desktop/olivia_home/rsrc/cyana/PCY.pdb -o PCY.lib Arrived 'olivia.update' from https://raw.githubusercontent.com/yokochi47/Olivia/master/legacy

Segmentation fault: 11 bash-3.2$ pdb2reslib -i/Users/adaligie/Desktop/olivia_home/rsrc/cyana/PCY.pdb -o PCY.lib Arrived 'olivia.update' from https://raw.githubusercontent.com/yokochi47/Olivia/master/legacy

Segmentation fault: 11

[yokochi47]

Hi Emilyada,

Sorry for your inconvenience. Unfortunately, the source PDB file is required to investigate the issue. Otherwise, could you plese report core-dump analysis using GNU debugger?

Thank you,

Masashi

[emilyada]

OK, I will try this, but I wonder, when I open olivia I always have the message below.

Couldn't get environment variable $NMRBIN.

do you think that it might cause problem