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

From: Jason Swails <>
Date: Fri, 18 Feb 2011 08:27:19 -0500


>From looking at the log file, it appears to me like you tried loading the amber prep file, but never the frcmod file that goes along with it. Make sure you use the command "loadamberparams my.frcmod" for whatever name your frcmod file may have.

I also never saw you try to save the amber topology file with "saveamberparm unit prmtop inpcrd". Do you get any errors trying to do this?

Good luck,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
On Feb 18, 2011, at 12:31 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.
> <metals.mpeg>
> <metals.prp>
> <leap.log>
> <new.pdb>
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Received on Fri Feb 18 2011 - 05:30:04 PST
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