Dear Openbabel community, I have a pdbqt (after vina docking) of a +vely charged compound which I'm reducing and converting into mol2 format with gasteiger charges. But the sum of charges in mol2 files is almost zero, not +1 as expected. I also tried using --gen3D flag and other charge models e.g. qeq, mmff94 during the conversion but in vain. Some methods give -ve charge! (Files are attached and command given below).
Can you please suggest if there is a method in babel that can reliably
estimate net charges on molecules without manual intervention?
I want this to work since I have a workflow for docking and MD that is
working except for the fact that there is no reliable method to estimate
net-charge without visual inspection of the structure.
I've manually summed the charges in excel, it is zero, not +1.
Is it possible that I missed something trivial?
Looking forward to valuable suggestions from the community.
thank you and best regards
babel test.pdbqt -O test.mol2 -h -m --partialcharge gasteiger --gen3D
WARNING: damped steplength 0.0143888 to 0.00575672
WARNING: damped steplength 0.00447914 to 0.00300176
9 molecules converted
9 files output. The first is test1.mol2
3621 audit log messages 99 debugging messages
Command to print netcharge (uses "st" from github).
egrep -A1000 ATOM test1.mol2 | grep -v ROOT | grep LIG | sed -e "1d" | awk
'{print $9}' | st | awk '{print $4}' | tail -1 | xargs printf "%1.0f" &&
echo ""
-0
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.di...@pilani.bits-pilani.ac.in, vaibhavadi...@gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
NCBI bibliography:
https://www.ncbi.nlm.nih.gov/myncbi/1Jgo56b26_AYKd/bibliography/public/
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
P Please consider the environment before printing this e-mail
test.pdbqt
Description: Binary data
test1.mol2
Description: chemical/mol2
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