AMBER Archive (2009)

Subject: Re: [AMBER] Re: AMBER: ligand parameter

From: Bo Baker (ratuma2009_at_gmail.com)
Date: Tue Jan 06 2009 - 23:05:00 CST

Hi, Ross:

> What do you mean by this step: 'I manually changed the "DU" to the
atomtype...'

In the first .prep:
  16 C7M DU E 15 14 13 1.509 120.318 176.719 0.000
  17 C8 c2 M 15 14 13 1.399 120.379 -0.857 0.000
  18 C8M DU E 17 15 14 1.517 117.888 178.625 0.000

I changed "DU" to :

  16 C7M c3 E 15 14 13 1.509 120.318 176.719 0.000
  17 C8 c2 M 15 14 13 1.399 120.379 -0.857 0.000
  18 C8M c3 E 17 15 14 1.517 117.888 178.625 0.000

> You shouldn't have to change anything in the prep file

I tried the unchanged .prep to generate .parm file. When I load it, amber
complains:

> loadamberprep FAD4.prep
Loading Prep file: ./FAD4.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

At the end, amber complains the bond problem, and not save the parm file.

I have the prep files (FAD4.prep and FAD4a.prep (with DU changed) attached
along with the log file.

Thank you for your advice.

Bo

On Wed, Jan 7, 2009 at 3:25 PM, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> Hi Bo,
>
> > 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
>
> What do you mean by this step: 'I manually changed the "DU" to the
> atomtype...'
>
> You shouldn't have to change anything in the prep file and I suspect this
> might be part of your problem since it is probably adding additional atoms
> that shouldn't be there. Do you mean the DU's in the following type of
> file:
>
> SUS INT 0
> CORRECT OMIT DU BEG
> 0.0000
> 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
> 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
> 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
> 4 C2 ca M 3 2 1 1.540 111.208 180.000 -0.17826
> 5 C1 ca M 4 3 2 1.386 86.897 -162.979 -0.04968
> ...
>
> If so you should not mess with these they are used to define the z-matrix
> that describes the structure of the custom residue. Did you follow the
> procedure described here: http://ambermd.org/tutorials/basic/tutorial4/ ?
>
> > 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.
>
> You are getting a parm and inpcrd file but it won't be of any use due to
> the
> long bonds. The problem is almost certainly in the prep files. If you can
> send one of them it would help but I would start by making sure you follow
> the procedure as described in the tutorial (and don't edit the resulting
> prep file you shouldn't need to).
>
> Grep out each residue in turn from the protein pdb file and use this single
> residue pdb as the input to antechamber.
>
> > 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.
>
> No it should not be ignored... As soon as you try to do MD you system will
> blow up due to the huge bond energies you will get.
>
> All the best
> 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 |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
>
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  • application/octet-stream attachment: FAD4.prep




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