[AMBER] Error in leap on using divalent ion

From: Chayya Bhargac <chayyachemistry.gmail.com>
Date: Wed, 9 Aug 2017 09:23:42 -0400

Hello,

I am trying to use polarizable forcefield ff02 for a protein with 1 Mg2+
and 1 Ca2+ . I am trying to parametrize the Ca to create a .lib and .frcmod
file.
For MG, I used the library from ions94.lib. For Ca I used the library file
for MG and changed some of the parameters.

When I try to run the leap file, I get an error:

Loading library: ./MG.lib

Loading PDB file: ./4Ca_CaM_pqr.pdb

Unknown residue: MG number: 144 type: Terminal/beginning

..relaxing end constraints to try for a dbase match

  -no luck

Unknown residue: Ca number: 145 type: Terminal/last


FATAL: Atom .R<MG 148>.A<MG 1> does not have a type.

FATAL: Atom .R<Ca 149>.A<Ca 1> does not have a type.


Failed to generate parameters

Parameter file was not saved.



I have attached my tleap file and .frcmod for Ca and MG and library file
(saved as Ca.dat and MG.dat for security restrictions by gmail). Please let
me know what I am doing wrong in setting this up.



Thank you,

Chayya Bhargava


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Received on Wed Aug 09 2017 - 06:30:02 PDT
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