Hello,
according to .mpg and .prp files, calcium ion in PDB must have atom
name KA and residue name CAL,
Here is example:
TER
HETATM 6159 KA CAL B1568 23.187 -16.230 6.242
TER
On Fri, Feb 18, 2011 at 8:31 AM, Aditya Padhi <adi.uoh.gmail.com> 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
> 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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>
--
Dmitry Nilov,
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
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Received on Wed Mar 02 2011 - 03:30:02 PST
