Dear Yasuo Kurita,
------------------------------------------------------------------------------------------------------------------------------
> I am trying to make an equilibrium calculation of 1EMB.pdb for
> preparing Gaussian09 code
> "SAC-CI ONIOM" calculation of GFP chromophore to get a light
> emitting spectra.
> The Residue type of chromophore is CRO which is not a standard Amino
> acid residue.
> So "saveamberparm" command reject to make the top and res files.
> Could you let me know how I can solve this problem?
You need to create a force field library (with atom names, topology,
charges, atom types etc...) for your chromophore.
If this is a non-standard amino-acid (AA*) residue you need to create
a molecular fragment for this AA* to be connected with the other AA
residue belonging to your protein.
This molecular fragment is in general built from a dipeptide; i.e. the
molecular fragment for this AA* is capped with the Acetyl and
NH-methyl group: suc as: ACE-AA*-NME
Charge derivation allows you to generate the fragment AA* starting
from ACE-AA*-NME
See Tutorial . q4md-forcefieldtools.org and in particular in the order:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
then
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#16
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#17
then
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
and finally
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
regards, Francois
See comments below as well.
------------------------------------------------------------------------------------------------------------------------------
> GFP(Green Fluorescence Protein) is now widely used in bio-technology world.
> GFP chromophore is protected by a beta sheet barrel and kept in
> appropriate structure
> by surrounding residues and one water.(Hydrogen bond network)
> GFP chromophore + beta barrel Xray structure is in Protein Data Bank
> named 1EMB.
> I picked 1EMB.pdb and chopped REMARK cards etc,only ATOM cards HETATM cards
> ,and a TER card an END cards left.
> HETATM cards(GFP chromophore) were located in the middle of ATOM
> cards(barrel).
> I used leap
> 1. tleap -f $AMBERHOME/dat/leap/cmd/leaprc.ff03
> 2. gfpgfp=loadpdb ./1EMB.pdb
> one hevy atom and about 1800 protons added
> 3.alignaxes gfpgfp
> 4.solvate box gfpgfp TIP3PBOX 10
> 5.charge gfpgfp
> Total unperturbed charge: -6
> 6.addions gfpgfp Na+ 0
> 7.saveamberparm gfpgfp gfpgfp.top gfpgfp.res
> But res file and top file wre not created,because of residue type
> CRO was not in the standard residue type file.
So you need to create a new force field library for this
post-translational modification.
> GFP chromophore is tyrosine and histidine,but peptide junction part
> was removed by post-translation process.
> If I changed residue names TYR instead of CRO and histidine part HIS.
> loadpdb command insert heavy atoms of junction part.
> I want leap just assign appropriate force fields to ATOM cards
> containing CRO .
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Received on Fri Feb 17 2012 - 23:00:02 PST
