AMBER Archive (2007)

Subject: AMBER: Copper and Chlorine parameters

From: Syed Tarique Moin (tarisyed_at_yahoo.com)
Date: Tue Sep 25 2007 - 05:39:16 CDT

Hello,

I built parameter for these like this procedure,as in
your another mail

Calcium has the atom type C0
 
See line 18 of $AMBERHOME/dat/leap/parm/parm99.dat
 
C0 40.08 calcium
This confusing atom type assignment is because CA is
used for aromatic carbons.
 
The second issue is that for some reason there is not
calcium residue defined. So you will need to build
this yourself. This is fairly easy to do in xleap.
Firstly start xleap and load the frcmod.ff99SB file.
Then pick the residue name you want to use for the
calcium ions in your pdb file. I suggest Ca2. Then
 
edit Ca2
 
select draw and then other elements and then Calcium.
 
Then draw a single calcium ion in the leap edit
window.
 
Then choose "select", rubber band the calcium ion you
just created to highlight it.
 
Then Edit->Edit selected atoms.
 
Specify the name as Ca, the type as C0, and the charge
as +2.
 
Then Table->Save and Quit.
 
you can then save yourself a library file for use
later.
 
saveoff Ca2 Ca2.lib
 
Then edit your pdb file to make sure all the calcium
ions belong to residue name Ca2 and that they have
atom names of Ca. You may also want to add TER cards
between each ion.
 
Then you can load xleap again from scratch.
 
source leaprc.ff99SB
loadoff Ca2.lib
foo = loadpdb foo.pdb
 
If i did it right or wrong with this procedure for
copper and chloride.

but during loading its not giving this type of error
but during saving into topology or coordinate file it
gives the following error:
Building topology.
Building atom parameters.
For atom: .R<CU 601>.A<CU 1> Could not find type: CU
For atom: .R<CU 602>.A<CU 1> Could not find type: CU
Parameter file was not saved.

I am also attaching the leap.log file so that it could
be understand better.

Regards

Syed Tarique Moin,
Junior Research Fellow,
H.E.J. Research Institute of Chemistry,
International Center for Chemical and Biological Sciences,
University of Karachi, Karachi-75720, Pakistan

tarisyed_at_yahoo.com
tarisyed_at_hotmail.com

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