Re: [AMBER] MD simulation of protein with Calcium ion

From: Sangita Kachhap <>
Date: Fri, 18 Feb 2011 11:25:14 +0530 (IST)

You have .lib file and did you loadoff it after loading .frcmod?
You require .lib file to generate topology and inpcrd for protein having ca2+ ion.
first load .frcmod, .lib then finaly .pdb
You please again go through the tutorial.

Good Luck
> 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
> loaded the pdb into a new file and using
> *loadamberprep metals.prp* command, I added the ion parameter file from
> 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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Sangita Kachhap

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Received on Thu Feb 17 2011 - 22:00:05 PST
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