Hi all,
I am simulating a protein with calcium ion in it. I have removed all the
hydrogen prior to MD and added using tleap. Then as per the instructions at
http://enzyme.fbb.msu.ru/Tutorials/Tutorial_2/Sec_1.htm,<
http://enzyme.fbb.msu.ru/Tutorials/Tutorial_2/Sec_1.htm>I
loaded the pdb into a new file and using
*loadamberprep metals.prp* command, I added the ion parameter file from
http://www.pharmacy.manchester.ac.uk/bryce/amber. Then I saved the pdb file
but it is showing error like the following
mol = loadpdb new.pdb
Loading PDB file: ./new.pdb
Unknown residue: CA number: 355 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Creating new UNIT for residue: CA sequence: 356
Created a new atom named: CA within residue: .R<CA 356>
total atoms in file: 5555
The file contained 1 atoms not in residue templates
I tried but its showing the above error all the time. Kindly help me in
resolving the problem. I am attaching the protein PDB, prp, frcmod and leap
log file for reference.
Thank you.
Aditya.
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- application/octet-stream attachment: leap.log
Received on Thu Feb 17 2011 - 22:00:03 PST
