Bug: CORAL treats phosphoSer as two residues

Interactive modelling (MASSHA, SASpy) and global minimization programs (SASREF, BUNCH, CORAL, GLOBSYMM)
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Alex
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Bug: CORAL treats phosphoSer as two residues

#1 Post by Alex » 2014.07.04 14:11

Hi
I was using CORAL to do modeling using rigid body where SER was phosphorylated.
I used contact restraints. After a few attempts I noticed that the restraints are
not being kept properly. Careful inspection of the output model revealed that
phospho SER is being treated as two residues and hence it screwed up the
contact conditions I used. This still happens if I use HETATM instead of ATOM field
for the phosphorylated group - moreover, in output model CORAL changes
HETATM to ATOM.

If required I can provide my input file.
Best, Alex

SaxsMax
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Re: Bug: CORAL treats phosphoSer as two residues

#2 Post by SaxsMax » 2014.07.16 11:16

" Ca " and " P " are treated as backbone atoms.
This should be taken into consideration when composing the contacts conditions file.

Alex
Active member
Posts: 692
Joined: 2007.08.09 21:10
Location: Planet Earth

Re: Bug: CORAL treats phosphoSer as two residues

#3 Post by Alex » 2014.07.16 14:08

every phosphorylated amino acid would be considered as two residues then. Would not it be better to fix it such that CORAL
distinguishes it from nucleotide?

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