AMBER Archive (2005)

Subject: Re: AMBER: antechamber problem

From: bybaker_at_itsa.ucsf.edu
Date: Wed Sep 21 2005 - 19:55:45 CDT

('binary' encoding is not supported, stored as-is)

Hello, Junmi:

Thanks for your help.

I change the atom names manually, and then run it with 'antechamber'.
This time, I am able to create the .prep and parm files. Thanks!

But when I used these file to create the .prmtop and .ipcrd files, it
failed. Here is how I did:

guanine.8% $AMBERHOME/exe/tleap
-I: Adding /usr/local/amber7/dat/leap/prep to search path. 

---

Welcome to LEaP!
(no leaprc in search path)
> source leaprc.ff94
----- Source: /usr/local/amber7/dat/leap/cmd/leaprc.ff94
----- Source of /usr/local/amber7/dat/leap/cmd/leaprc.ff94 done
Log file: ./leap.log
Loading parameters: ./parm94.dat
----
> source leaprc.gaff
----- Source: /usr/local/amber7/dat/leap/cmd/leaprc.gaff
----- Source of /usr/local/amber7/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /usr/local/amber7/dat/leap/parm/gaff.dat
> mod = loadamberparams frcmod-2
Loading parameters: ./frcmod-2
Reading force field mod type file (frcmod)
> loadamberprep FAD-1a.prep
Loading Prep file: ./FAD-1a.prep
** This is a remark line: 'IMPROPER' atom C7M not found
** This is a remark line: 'IMPROPER' atom C8M not found
** This is a remark line: 'IMPROPER' atom N6A not found
> loadamberparams FAD-1a.parm
Loading parameters: ./FAD-1a.parm
Reading force field mod type file (frcmod)
> test = loadpdb POR-1a.pdb
Loading PDB file: ./POR-1a.pdb
 (starting new molecule for chain A)
  Added missing heavy atom: .R<CSER 620>.A<OXT 12>
Created a new atom named: AP within residue: .R<FAD 621>
Created a new atom named: AO1 within residue: .R<FAD 621>
Created a new atom named: AO2 within residue: .R<FAD 621>
---
---
Created a new atom named: O3P within residue: .R<FAD 621>
  Added missing heavy atom: .R<FAD 621>.A<N3A 49>
  Added missing heavy atom: .R<FAD 621>.A<C2A 48>
  ----
  Added missing heavy atom: .R<FAD 621>.A<PO1 27>
  total atoms in file: 5000
  Leap added 4842 missing atoms according to residue templates:
       25 Heavy
       4817 H / lone pairs
  The file contained 27 atoms not in residue templates
> saveAmberParm test POR-1a.prmtop POR-1a.inpcrd
Checking Unit.
WARNING: There is a bond of 4.049952 angstroms between: 
-------  .R<FAD 621>.A<C5A 45> and .R<FAD 621>.A<C6A 46>
---
---
WARNING: The unperturbed charge of the unit: -19.000000 is not zero.
FATAL:  Atom .R<FAD 621>.A<AP 51> does not have a type.
FATAL:  Atom .R<FAD 621>.A<AO1 52> does not have a type.
---
---
Failed to generate parameters
Parameter file was not saved.

The .pdb file includes the ligand. I have included it as an attachment.
Can you suggest what could be wrong with my file? 

Thank you very much

Bo

On Tue, 20 Sep 2005 18:05:36 -0500 "Junmei Wang" wrote:

> Hi, 
> Antechamber recognize element/atom type based on the atom names.
> Therefore, you may manually modify the atom names, for example, change
> AP to PA, A01 to O1A. 
> 
> Best regards
> 
> Junmei
> 
> 
> 
> 
> 
> Hello, Amber:
> 
> I try to load a ligand (named as FAD-1 here), and use abtechamber to
> creat prep file. Here is how I did:
> 
> guanine.1% setenv AMBERHOME /usr/local/amber7
> guanine.2% antechamber -i FAD.pdb -fi pdb -o FAD.prep -fo prepi
> 
>  Unrecognized atomic name  AP  , exit
>  Unrecognized atomic name  AO1 , exit
>  Unrecognized atomic name  AO2 , exit
> -------
> 
> 
> I search the mail list, but hard to find the answer. I have included the
> pdb file as an attachment. I use Amber7.
> 
> Thanks for any suggestion. 
> 
> 
> 
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