Dear all,
this is kind of a follow up of the "cis proline cipp patch" email from
last Friday.
I have 2 cis-prolines (as judged from chemical shifts and NOE
connectivities) in my structure.
I am using CNS and this topology and parameter file:
topallhdg5_3.pro
parallhdg5_3.pro
I could get around my original problem (that was to create an cis mtf
file) by mending the topallhdg5_3.pro file.
So in the end I managed to get a cis-mtf file.
The difference between the mtf-file and the cis-mtf file is the
following:
mtf-file 324 ' ' ' 707 ' 'PRO' 'C' 'C'
0.500000 12.0110
cis-mtf file 324 ' ' ' 707 ' 'PRO' 'C' 'CCIS'
0.500000 12.0110 (the sequence goes: 707-trans-PRO ---
708-cis-PRO >> so it is correct
to change the 707-PRO 'C' to 'CCIS'
and
mtf-file 1802 ' ' ' 798 ' 'ASP' 'C' 'C'
0.500000 12.0110
cis-mtf-file 1802 ' ' ' 798 ' 'ASP' 'C' 'CCIS'
0.500000 12.0110 (the sequence goes: 798-ASP ---
708-cis-PRO)
So far so good!
New problems appeared when we tried to calculate the template pdb (this
uses parallhdg5_3.pro).
We got Error messages for "missing nonbonded Lennard-Jones parameters",
"missing dihedral parameters" and "missing improper parameters".
All these messages were complaining about NOT having dihedrals,
impropers and "nonbonded Lennard-Jones" with the CCIS atom type defined
in parallhdg5_3.pro (or possibly elsewhere ?) .
Fair enough, we had some CCIS values in our parallhdg5_3.pro, but for
the particular ones (dihedrals, impropers and nonbonded Lennard-Jones),
we got an error messages for, the definitions with the atom-type CCIS
were missing.
QUESTION 1:
Wherever there was a "template definition" like
DIHEdral CH2E CH1E C O MULT 6 0.375 1 0.0000 0.3 2
0.0000 0.225 3 0.0000 0.15 4 0.0000 0.075 5 0.0000 0.0375 6
0.0000 !aaa-aaa
I just copy-pasted the line and changed the 'C' in question to 'CCIS'
DIHEdral CH2E CH1E CCIS O MULT 6 0.375 1 0.0000 0.3 2
0.0000 0.225 3 0.0000 0.15 4 0.0000 0.075 5 0.0000 0.0375 6
0.0000 !aaa-aaa
with the exception of the actual improper that defines the cis peptide
bond:
IMPRoper CH1E C N CH1E 500.00 {sd= 0.031}
0 179.9873
IMPRoper CH1E CCIS N CH1E 500.00 {sd= 0.031}
0 0.0000 !!!!! CIS PRO >> I changed value to 0.0
I have done this with every dihedral, improper and "nonbonded
Lennard-Jones" I have got an error message for and I could find a
template for. So the values for the
settings containing 'C' and 'CCIS' are the same.
IS THIS EXACTLY THE RIGHT THING TO DO?
I am grateful for any advice and comments!
QUESTION 2:
This really puzzles me:
There were 2 error messages asking for 2 IMPRopers which in its kind
haven't been defined in the original parallhdg5_3.pro.
A similar improper can be found in the topology-file (improper HA N C
CB !defining the chirality of CA), but I could not find any defining
values for this
in the parameter file. (And when I calculated structures with all PRO
set trans - just for comparison - there was no error message for these 2
IMPRopers meaning they are only used when calculation with the PRO set
cis ???)
So I had to "make them up" myself. Just in order to find out if I would
be able to create a template pdb, I just put a random value with a very
small "rating" value:
IMPRoper HA NH1 CCIS CH2E 0.1000 {sd= 0.031} 0
-72.1561
IMPRoper HA N CCIS CH2E 0.1000 {sd= 0.031} 0
-72.1561
Indeed, I got a template pdb and the subsequent structure calculation
went "alright".
DOES ANYONE HAVE THE RIGHT VALUES FOR THESE TWO IMPRopers OR WHAT
IS THE BEST METHOD OF GETTING THEM?
(WHY IS THERE A NEED TO DEFINE 2 MORE IMPRopers IN THE
cis-calculation WHEN THE trans-calculation DIDN'T NEED THEM?)
Again, I am grateful for any advice and comments!
If you are really interested in what and how many changes were needed to
get the cis-pdb-template, I could email you the 2 files parallhdg5_3.pro
(original) and cis-parallhdg5_3.pro (mended) for comparison.
Thanks a lot and Kind Regard,
Christoph
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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