[Xplor-nih] MTSL-labeled denatured protein and ensemble calculation

[Charles at Schwieters.org]

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Hello Jie-rong--

I'm replying to the list, because it may help others.

> 
> First, I tried to use (eginput/PSF_generation) addAtoms.py to add MTSL, but I
> couldn't get a folded structure as shown in your example files. 
> 
> Here is some lines of pdb file I input
> ===
> ATOM    16    HG1    MET    1    26.311    24.347    5.363    0    0
> ATOM    17    HG2    MET    1    25.43    25.902    5.514    0    0
> ATOM    18    HE1    MET    1    23.706    23.466    8.265    0    0
> ATOM    19    HE2    MET    1    25.427    23.475    7.749    0    0
> ATOM    20    HE3    MET    1    24.552    25.026    7.991    0    0
> ATOM    21    HY1    MET    1    28.543    23.329    2.359    0    0
> ATOM    22    HY2    MET    1    29.629    24.547    2.219    0    0
> ATOM    23    HY3    MET    1    28.842    23.995    0.893    0    0
> ATOM    24    N        GLN    2    26.335    27.77    3.258    1    0
> ATOM    25    CA      GLN    2    26.85    29.021    3.898    1    0
> ATOM    26    C        GLN    2    26.1    29.253    5.202    1    0
> ATOM    27    O        GLN    2    24.865    29.024    5.33    1    0
> ATOM    28    CB      GLN    2    26.733    30.148    2.905    1    0
> ATOM    29    CG      GLN    2    26.882    31.546    3.409    1    0
> =====
> 
> This proton-added file is generated from NAMD psfgen script, the main
> difference comparing to example file is the final two columns (I think they
> are size and charge).  Is it the reason?  If yes, how to generate a suitable
> pdb file as xplor input? 
> 

Are you saying you can't get the addAtoms script to read a
NAMD-generated pdb? It's had to say what's wrong without seeing the
error messages. On the other hand if, in that script, you replace the
addUnknownAtoms command with 
protocol.genExtendedStructure()
a valid pdb will be created- but with an extended protein structure.

> Second question is, how to use PRE information I have to calculate the
> sturcture?  Originally, I thought it would be like using NOE as distance
> restraints and annealing protocol such as "sa.inp", but I also saw
> "PMAGnetic" command in the manual......  Could you give me a hint, example
> scripts, or point me to some tutorial files for this kind of calculation?  

Please see 
http://spin.niddk.nih.gov/clore/Software/pre_distribute.tar.Z
for a full example. If you have further questions, please contact me. I
do intend to include that example in the Xplor-NIH distribution at some
point.

best regards--
Charles
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