Hello,
I am trying to use XPLOR-NIH to model a lassopeptide.
I have code that works for one of my peptides. I have attached this below.
However, if I change the sequence, the output PSF file no longer works for
XPLOR-NIH calculations. Instead of calculating and generating PDB files, it
gives the error attached below. This is very confusing. I'm not sure what I am
doing wrong.
Are there any suggestions you have for fixing this issue?
Many thanks,
Brett
rtf @TOPPAR:protein.top end
parameter
@TOPPAR:protein.par
{* $kbon, $kang and $kchi are defined in this file *}
end {*Read topology file *}
segment {*Generate protein *}
name="temp" {*This name has to match the *}
{*four characters in columns 73 *}
{*through 76 in the coordinate *}
{*file, in XPLOR this name is *}
{*name is referred to as SEGId. *}
chain
@TOPPAR:toph19.pep {*Read peptide bond file *}
sequence GLY ALA GLY THR ALA ARG GLU ARG ASP LEU LEU GLY PHE ARG ALA LEU
ILE VAL ILE HIS TRP PRO TRP LEU
end
end
topology
presidue ISON ! isopeptide linkage - mod of ISOP - N terminal
! 2014/09/09 + is N-term - is ASP
group
modify atom -CG charge = 0.480 end
modify atom -OD1 type=O charge = -0.480 end
delete atom -OD2 end
group
delete atom +HT3 end
delete atom +HT2 end
delete atom +HT1 charge = 0.260 end
add atom +HN type=H charge = 0.260 end
modify atom +N type=NH1 charge = -0.360 end
add bond -CG +N
add bond +N +HN
add angle -CB -CG +N
add angle -OD1 -CG +N
add angle -CG +N +CA
add angle -CG +N +HN
ADD DIHEdral -CB -CG +N +HN
ADD DIHEdral -CB -CG +N +CA
ADD DIHEdral -OD1 -CG +N +HN ! double dihedral
ADD DIHEdral -OD1 -CG +N +HN ! double dihedral
ADD DIHEdral -OD1 -CG +N +CA
add improper -OD1 -CG +N +CA
add improper -CB -CG +N +CA
end
patch
ISON
reference=+=( resid 1 ) reference=-=( resid 9 )
end
end
write structure output=Lasso_SORA.psf
end
stop
ERROR if I change sequence:
[cid:f1e7ee75-502f-4906-81fd-1806d065e250]
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