AMBER Archive (2006)

Subject: RE: AMBER: problem in saving parameter file for non-standard residue

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Jan 16 2006 - 10:44:11 CST

Dear Priti,

> I have actually followed your tutorial five to get the
> parameters. I used
> the following commands:
>
> source leaprc.gaff
> loadamberprep major.resp.prepin
> loadamberparams major.frcmod

> Do I need to use "loadamberparams gaff.dat" in addition to "source
> leaprc.gaff" ? Also, I mentioned in my first mail that I
>have been able to

No, you do not, the leaprc files are scripts that load both the templates
for specific residues and the parameter files. However, if say you wanted to
use the FF94 force field for you protein but the GAFF force field for your
ligand then you would do:

source leaprc.ff94
loadamberparams gaff.dat

sourcing both the leaprc.ff94 script and the leaprc.gaff script could cause
problems and so it is best to avoid this. I hope this makes sense.

> the non-standard residue. However, when I include that in
> the PDB and try
> to save the prmtop file, it gives those bond, angle and
> torsion problem.
> Also, my non-standard residue is a modified Serine residue.
> That means
> that backbone connection is same as should in the case of standard
> residues. For your reference, I am attaching a pdb file
> containing the
> non-standard residue with two residues each before and after that.

The issue is that when you include it in the PDB bonds are being made
between your protein and your antechamber ligand. This means that parameters
for those bonds and newly created angles and dihedrals are now required.
These are the parameters that are missing. Leap distinguishes case so for
example while:

H-N-CT exits H-N-ct does not. You need to define these missing parameters.

Since you do indeed want the backbone connections to be present then you can
simply provide these missing parameters in an frcmod file - the one that
antechamber created for you would be fine. Just add the parameters in the
relevant positions. You can probably safely assume that the backbone
parameters are unaffected by the modifications so just copy the standard
backbone parameters.

You may want to also check, just to be sure, that the correct bonds are
being made. I find it is often useful to draw out on a sheet of paper your
modified residue and then the two residues that are adjacent to it. You can
then write in the atom types and work out which bond, angle and dihedrals
terms you expect to be missing and what terms they would represent if your
serine was an unmodified residue.

I hope this helps.
All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | 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.

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Priti Hansia
> Sent: Friday, January 13, 2006 20:29
> To: amber_at_scripps.edu
> Cc: Ross Walker
> Subject: RE: AMBER: problem in saving parameter file for
> non-standard residue
>
> Forgot to attach the pdb file. Here it is.
>
>
>
> > Dear Ross,
> >
> > I have actually followed your tutorial five to get the
> parameters. I used
> > the following commands:
> >
> > source leaprc.gaff
> > loadamberprep major.resp.prepin
> > loadamberparams major.frcmod
> >
> > Do I need to use "loadamberparams gaff.dat" in addition to "source
> > leaprc.gaff" ? Also, I mentioned in my first mail that I
> have been able to
> > create the parameter file for the non-standard residue when I don't
> > include that in the actual PDB, i.e., prmtop file can be
> saved just for
> > the non-standard residue. However, when I include that in
> the PDB and try
> > to save the prmtop file, it gives those bond, angle and
> torsion problem.
> > Also, my non-standard residue is a modified Serine residue.
> That means
> > that backbone connection is same as should in the case of standard
> > residues. For your reference, I am attaching a pdb file
> containing the
> > non-standard residue with two residues each before and after that.
> >
> > Please clarify my doubts.
> >
> > Thanks,
> > -Priti
> >
> >
> >
> >
> >
> >> Dear Priti,
> >>
> >> If you used antechamber to build your non-standard residue
> then it will
> >> have
> >> defined the atom types and any missing parameters based on the gaff
> >> force
> >> field. This force field can be used in addition to the regular FFXX
> >> force
> >> fields since it uses lower case atom types. In this case
> your parameters
> >> have not been found because you did not load the gaff.dat file into
> >> leap.
> >>
> >> Start Leap as you have been doing and then before you load your non
> >> standard
> >> residue and pdb etc type:
> >>
> >> loadamberparams gaff.dat
> >>
> >> You should then be able to load your non-standard residue
> and pdb and
> >> then
> >> save the prmtop file.
> >>
> >> Note, you may also need to load the frcmod file
> antechamber created if
> >> necessary. You should also look at the atom types and parameters
> >> antechamber
> >> assigned with reference to the GAFF force field paper and
> make sure they
> >> are
> >> what you would expect...
> >>
> >> Note: you should probably work through the following tutorial:
> >>
> >>
> http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_
> five/index.htm
> >>
> >> This will give you a better understanding of what
> Antechamber is doing.
> >>
> >> All the best
> >> Ross
> >>
> >> /\
> >> \/
> >> |\oss Walker
> >>
> >> | Department of Molecular Biology TPC15 |
> >> | The Scripps Research Institute |
> >> | Tel: +1 858 784 8889 | 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.
> >
> >
>

http://www.rosswalker.co.uk/star_wars_sounds/
/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | 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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