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

From: Dmitry Nilov <>
Date: Wed, 2 Mar 2011 14:02:46 +0300

according to .mpg and .prp files, calcium ion in PDB must have atom
name KA and residue name CAL,

Here is example:

HETATM 6159 KA CAL B1568 23.187 -16.230 6.242

On Fri, Feb 18, 2011 at 8:31 AM, Aditya Padhi <> wrote:
> 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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Dmitry Nilov,
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
AMBER mailing list
Received on Wed Mar 02 2011 - 03:30:02 PST
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