Dear Amber Users and Developers,
I am working
on a CNT functionalized with a HIP residue. I have made a off file using
xleap where all the charges of C and H atom of CNT is zero. And the charges
of atoms of HIP residue is taken from HIP library file. To make the total
charge +1 I have changed the charge of CB atom of HIP. Now, when I am going
to make prmtop and inpcrd file from xleap I am facing a problem. I upload
the off file first, then the pdb file, and then solvate it. Then I add a
Cl- ion to make the system neutralized. Then when I am giving the command
"saveamberparm cnt cnt_hip.prmtop cnt_hip.inpcrd" i am getting the
following error.
> saveamberparm cnt cnt_hip.prmtop cnt_hip.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
For atom: .R<Cl- 4897>.A<Cl- 1> Could not find type: Cl-
Parameter file was not saved.
why is this coming? Here xleap can not detect the Cl- ion.
Sanjib Paul
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Received on Sat Feb 09 2013 - 04:30:02 PST
