AMBER Archive (2004)

Subject: AMBER: atoms not in residue templates

From: Yongzhi Chen (yongzhi_mms_at_yahoo.com)
Date: Wed Aug 04 2004 - 12:53:08 CDT

Dear Amber users/developers,

I found Awasthi asked this question before but I could
not find the answer. The problem is as following. Leap
could not tell the atoms added by itself. I also
attach the pdb file.

> mol = loadpdb 1AVP.pdb
Loading PDB file: ./1AVP_C.pdb
Created a new atom named: H within residue: .R<NMET 1>
Created a new atom named: HD1 within residue: .R<HIE
36>
Created a new atom named: HD1 within residue: .R<HIE
54>
Created a new atom named: HD1 within residue: .R<HIE
131>
Created a new atom named: HD1 within residue: .R<HIE
143>
Created a new atom named: HD1 within residue: .R<HIE
181>
Created a new atom named: HD1 within residue: .R<HIE
188>
Created a new atom named: HD1 within residue: .R<HIE
200>
Created a new atom named: H within residue: .R<NGLY
205>
  total atoms in file: 2124
  Leap added 1275 missing atoms according to residue
templates:
       1275 H / lone pairs
  The file contained 9 atoms not in residue templates

> saveAmberParm mol 1AVP.prmtop 1AVP.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: 10.000000
is not zero.
FATAL: Atom .R<NMET 1>.A<H 20> does not have a type.
FATAL: Atom .R<HIE 36>.A<HD1 18> does not have a
type.
FATAL: Atom .R<HIE 54>.A<HD1 18> does not have a
type.
FATAL: Atom .R<HIE 131>.A<HD1 18> does not have a
type.
FATAL: Atom .R<HIE 143>.A<HD1 18> does not have a
type.
FATAL: Atom .R<HIE 181>.A<HD1 18> does not have a
type.
FATAL: Atom .R<HIE 188>.A<HD1 18> does not have a
type.
FATAL: Atom .R<HIE 200>.A<HD1 18> does not have a
type.
FATAL: Atom .R<NGLY 205>.A<H 10> does not have a
type.
Failed to generate parameters
Parameter file was not saved.

Any suggestion will be appreciate.

Best,
Yongzhi

                
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  • application/x-zip-compressed attachment: 1AVP.zip
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