AMBER Archive (2003)

Subject: protonate problem

From: Venkata S Koppuravuri (kvsuneel_at_linus.bmb.wright.edu)
Date: Wed May 14 2003 - 12:17:39 CDT

Hi,
I am trying to get used to Amber5. i have got 2 questions
 
1. When i tried to protonate 1DPU.pdb which
   i downloaded from the PDB website i got the following error message

---------------------------
Here are the mystery protons from input file:

HG CYS 219 11.83 -1.71 -2.66
--------------------------

2. the second molecule that i am trying on is 1FGU. with this molecule i
have taken only subunit B and deleted the subunits A and C.
Protonate did work fine with this but when i try to get prmtop and prmcrd
files using leap i got the following error message

------------------------
 FATAL: Atom .R<CCYS 289>.A<HG 13> does not have a type.
 Failed to generate parameters
 Parameter file was not saved.
-----------------------

can anyone please help me with these errors

Regards
-Venkat