From: Jason Richard Mick (dw2413_at_wayne.edu)
Date: Thu May 06 2010 - 17:23:54 CDT
Hi all,
I'm struggling with how best to generate the coordinates of a custom of a novel polypeptide derivative (a peptide amphiphile). There's two crucial modifications to the polypeptide -- a serine phosphorylation and a carboxylic acid tail added to the amino-terminus.
I created a custom patch residue as follows
...........................................
PRES TAI 0.00 ! carboxyl alkylated N-terminus
GROUP ! use in generate statement
ATOM CA1 CT2 -0.27 !
ATOM HA1 HA 0.09 ! |
ATOM HA2 HA 0.09 ! CY=OY
ATOM HA3 HA 0.09 ! |
GROUP !HA30-CA15-HA31
ATOM CA2 CT2 -0.18 ! |
ATOM HA4 HA 0.09 ! ...
ATOM HA5 HA 0.09 ! |
GROUP !HA1--CA1--HA2
ATOM CA3 CT2 -0.18 ! |
ATOM HA6 HA 0.09 ! HA3
ATOM HA7 HA 0.09 !
GROUP !
ATOM CA4 CT2 -0.18 !
ATOM HA8 HA 0.09 !
ATOM HA9 HA 0.09 !
GROUP !
ATOM CA5 CT2 -0.18 !
ATOM HA10 HA 0.09 !
ATOM HA11 HA 0.09 !
GROUP !
ATOM CA6 CT2 -0.18 !
ATOM HA12 HA 0.09 !
ATOM HA13 HA 0.09 !
GROUP !
ATOM CA7 CT2 -0.18 !
ATOM HA14 HA 0.09 !
ATOM HA15 HA 0.09 !
GROUP !
ATOM CA8 CT2 -0.18 !
ATOM HA16 HA 0.09 !
ATOM HA17 HA 0.09 !
GROUP !
ATOM CA9 CT2 -0.18 !
ATOM HA18 HA 0.09 !
ATOM HA19 HA 0.09 !
GROUP !
ATOM CA10 CT2 -0.18 !
ATOM HA20 HA 0.09 !
ATOM HA21 HA 0.09 !
GROUP !
ATOM CA11 CT2 -0.18 !
ATOM HA22 HA 0.09 !
ATOM HA23 HA 0.09 !
GROUP !
ATOM CA12 CT2 -0.18 !
ATOM HA24 HA 0.09 !
ATOM HA25 HA 0.09 !
GROUP !
ATOM CA13 CT2 -0.18 !
ATOM HA26 HA 0.09 !
ATOM HA27 HA 0.09 !
GROUP !
ATOM CA14 CT2 -0.18 !
ATOM HA28 HA 0.09 !
ATOM HA29 HA 0.09 !
GROUP !
ATOM CA15 CT2 -0.18 !
ATOM HA30 HA 0.09 !
ATOM HA31 HA 0.09 !
GROUP !
ATOM CY C 0.51 !
ATOM OY O -0.51 !
!
BOND CY CA15 CY N CA15 HA30 CA15 HA31
BOND CA14 CA15 CA14 HA28 CA14 HA29
BOND CA13 CA14 CA13 HA26 CA13 HA27
BOND CA12 CA13 CA12 HA24 CA12 HA25
BOND CA11 CA12 CA11 HA22 CA11 HA23
BOND CA10 CA11 CA10 HA20 CA10 HA21
BOND CA9 CA10 CA9 HA18 CA9 HA19
BOND CA8 CA9 CA8 HA16 CA8 HA17
BOND CA7 CA8 CA7 HA14 CA7 HA15
BOND CA6 CA7 CA6 HA12 CA6 HA13
BOND CA5 CA6 CA5 HA10 CA5 HA11
BOND CA4 CA5 CA4 HA8 CA4 HA9
BOND CA3 CA4 CA3 HA6 CA3 HA7
BOND CA2 CA3 CA2 HA4 CA2 HA5
BOND CA1 CA2 CA1 HA2 CA1 HA3
BOND CA1 HA1
DOUBLE OY CY
..............................
And I got the serine phosphate patch from the charmm repository. I'm guessing I need to generate the file using something like
..........................
psfgen <<ENDMOL
topology top_all27_prot_lipid.inp
segment PA1 {
pdb peptide_amphiphile.pdb
first TAI
last CTER
}
patch SP2 PA1:5
writepsf peptide_amphiphile_2.psf
writepdb peptide_amphiphile_2.pdb
...................
But I'm not sure what software tools I can use to make my PDB. My version of VMD has molefacture, but it does not support custom patching (just standard sequencing of residues). I also tried Gaussian 2009, but it did not output a PDB file with the proper residue names.
Right now I'm taking my Gaussian '09 structure and entering in resnames/resids by hand to the resulting PDB and renaming the atoms by hand to match the topology file names, but that's a pretty sad state of affairs.
My lab members all work regularly with VMD/NAMD/Gaussian, but none of them had any idea what tool to use. What tool would you suggest for generating a PDB with custom patching?
And does my PSFGEN script look roughly correct?
Thank you very much in advance!
Cheers,
Jason Mick
Wayne State University
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