[AMBER] MD simulation of protein with Calcium ion

From: Aditya Padhi <adi.uoh.gmail.com>
Date: Fri, 18 Feb 2011 11:01:28 +0530

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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Received on Thu Feb 17 2011 - 22:00:03 PST
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