Dear All,
I want to find the number of water molecules that are in direct contact
with the K+ ions in each frame during the simulation. I think this is not
supposed to remain constant since K+ ions will have occasional ion pairs
with counter ions, thus reducing the number of waters interacting with it.
For higher salt concentration, I should get a higher frequency of the
ion-pairs and thus a lower number of water contacts. Is this correct
thinking?
For this, I'm trying to use the nativecontacts command with the following
option, but it gives an error that the water mask corresponds to 0 atoms.
I tried giving residue numbers for all waters, but that also fails in
cpptraj
Is it possible to do this with the closest option? I think it gives the
residue number for waters that are within a certain distance, but I want to
count the number of waters that are in direct contact with K+ ions.
Please do suggest which command in cpptraj can help me get this analysis
done.
thank you and best regards
nativecontacts name KWAT :K+ :WAT byresidue out KWATcontacts.dat mindist
maxdist distance 4.0 first map mapout KWATresmap.gnu
contactpdb KWATcontactmap.pdb series seriesout KWATnativecontacts.dat
writecontacts KWATwritecontacts.dat
Mask [:K+] corresponds to 145 atoms.
Mask [:WAT] corresponds to 0 atoms.
Warning: Setup incomplete for [nativecontacts]: Skipping
nativecontacts name KWAT :K+ :876-23348&!.H= byresidue out KWATcontacts.dat
mindist maxdist distance 4.0 first map mapout KWATresmap.gnu
contactpdb KWATcontactmap.pdb series seriesout KWATnativecontacts.dat
writecontacts KWATwritecontacts.dat
Mask [:K+] corresponds to 145 atoms.
Mask [:876-23348&!.H*] corresponds to 0 atoms.
Warning: Setup incomplete for [nativecontacts]: Skipping
Regards,
Dr. Vaibhav A. Dixit,
Asst. Prof., Department of Medicinal Chemistry,
National Institute of Pharmaceutical Education and Research, Guwahati
(NIPER-G), Sila Katamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup, Pin:
781101, Assam, India
Mob. No. +91-7709129400,
Email: vaibhav.niperguwahati.in; vaibhavadixit.gmail.com
https://niperguwahati.ac.in/DOC/profile/dixit.pdf
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
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Received on Wed Jan 12 2022 - 23:00:02 PST
