Dear Sirs
This is Yasuo Kurita,a research scientist,in Physics Department of Tokyo University of Science.
Thank you very much for your kind collaboration in advance.
I want to add some more information to my old message;
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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?
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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.
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 .
I am very sorry to bothering you so much.
Your kind suggestion would be very much appreciated.
Thank you very much and best regards
Y.Kurita
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Received on Fri Feb 17 2012 - 03:30:02 PST
