AMBER Archive (2009)

Subject: [AMBER] Re: AMBER: ligand parameter

From: Bo Baker (ratuma2009_at_gmail.com)
Date: Tue Jan 06 2009 - 21:59:19 CST

Hi, Ross:

Thank you very much for your advice and detailed instructions.

> How did you prepare the pdb file for each residue that you fed to
Antechamber?

I extract the ligand pdb from the crystal structure, and fed them to
antechamber.
With the .prep files, I manually changed the "DU" to the atomtype based on
.gaff file, and use the modified .prep file to generate .parm files

> Were the coordinates the same / similar as what you now have in your
protein pdb file? Were the atom names the same and the order the same?

In the .prep files, the lignad coordinates are same as in protein pdb, but
the orders are different.

>I would also double check that you have TER between each of the residues
(top and bottom) in the actual pdb file that you are loading.

This time, I add a line such as "TER 5002 FAD 621" at the end of
each ligands.

>If would also try breaking the problem down. Load just the prep file for
FAD and a cut down pdb containing just FAD and see what happens.

I also try as above.

Here are the results:

With the three ligands and FAD only, amber complains the same bond problems.

I notice that when I load the protein, amber add some atoms. When I try to
save amberparm, it complains the bond problems with these added atoms. At
the end, the parm was created and saved.

It seems that the bond problem is associated to the atoms that are added by
amber. Should the warning be ignored? As the parm files are created and
saved at the end.

I use AMBER7 and have the file attached.

Thank you for your comment.

Bo

---------- Forwarded message ----------
From: Ross Walker <ross_at_rosswalker.co.uk>
Date: Tue, Jan 6, 2009 at 4:48 PM
Subject: RE: AMBER: ligand parameter
To: amber_at_scripps.edu

Hi Bo,

> I try to build amberparm with my target protein and the ligands. I used
> antechamber to build the prep and parm for each ligands, and loaded them
> together with .ff99. When I try to save amberparm, the program complains
>
> WARNING: There is a bond of 16.699220 angstroms between:
> ------- .R<FAD 621>.A<C4A 53> and .R<FMN 622>.A<O4 1>
> WARNING: There is a bond of 16.116888 angstroms between:
> ------- .R<FAD 621>.A<N3A 52> and .R<FAD 621>.A<C4A 53>
> WARNING: There is a bond of 16.770245 angstroms between:
> ------- .R<FAD 621>.A<C5A 47> and .R<FAD 621>.A<C6A 48>
> WARNING: There is a bond of 14.378186 angstroms between:
> ------- .R<FAD 621>.A<N7A 46> and .R<FAD 621>.A<C5A 47>
> WARNING: There is a bond of 13.779173 angstroms between:
> ------- .R<FAD 621>.A<C4A 8> and .R<FAD 621>.A<N9A 44>
> WARNING: There is a bond of 23.963962 angstroms between:
> ------- .R<FMN 622>.A<O1P 31> and .R<NAP 623>.A<NO1 1>
>
> I add "TER" at the end of each ligand in protein pdb file. I don't
> understand why there are bonds among these ligands. I guess that the parm
> files are not generated properly. I use Amber7.

If you notice most of the erros are for bonds within the same residue. For
example the second warning is for a 16 angstrom bond between N3A and C4A
within the same FAD residue. My guess is that the actual prep file itself is
bad. How did you prepare the pdb file for each residue that you fed to
Antechamber? Did you cut that residue out of the pdb? Were the coordinates
the same / similar as what you now have in your protein pdb file? Were the
atom names the same and the order the same? The order shouldn't strictly
matter but it will help. If would also try breaking the problem down. Load
just the prep file for FAD and a cut down pdb containing just FAD and see
what happens.

I would also double check that you have TER between each of the residues
(top and bottom) in the actual pdb file that you are loading. I know you say
you do but it doesn't hurt to double check. Also take a look at the pdb file
itself and make sure it looks reasonable - visualize it in something like
VMD to make sure it looks okay. I would also try loading the prep files into
leap and then type edit NAP or edit FMN and see what comes up - this will at
least show you if the prep files are reasonable.

The take home message: Try to break things down into smaller units that you
can tick off one by one before trying the entire protein pdb.

Good luck,
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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