I am new to JChem and started looking
at the examples for GenerateMD
(http://www.chemaxon.com/jchem/doc/user/GenerateMD.html). When I run (on Fedora 18)
generatemd c molecules/nci1000.sdf -o
nci1000.sdf -S -k PF -c config/pharma-frag.xml
(example 3), only one
new tag (<PF>) is generated in the output file, the <PMAP>
tag is missing.
Similarly, when executing
'generatemd_example' (in JChem/Examples/bin from JChem for end users
and Java developers, version 6.0.2), the output file nci1000-PF.sdf
does not contain <PMAP> tags, and the displayed structures are
Do I have to change something in the
Thank you for reporting this issue, we could reproduce it. We will try to solve it as soon as possible.
I have fixed this issue. The fix will be available in the 6.1 or in the 6.2 version.
If you want to find only pharmacophore points (and display these using MarvinView), please visit the following link:
http://www.chemaxon.com/jchem/doc/user/PMapper.html (Example 4.)
Or use the following commands:
pmapper -c config/pharma-frag.xml -o nci1000.sdf -S molecules/nci1000.sdf
mview -t PMAP -p config/PF.colors nci1000.sdf
Thanks explaining an alternative
option. Could you point out where I could find a summary of the
command line tools?