his FAQ answers common questions regarding the use of MCCE program and the
underlying physics in a definitive and succinct style. It is not intented to
substitute a full-length reference manual.
Questions are divided into the following categories:
- Setting up a run
- Understanding MCCE
Latest question is highlited in red.
Section 1. Installation
1.1 How to uninstall mcce?
Delete the directory of MCCE will clean all the installed programs. Sometimes you want to delete the MCCE directory in your search path defined by environment variable $PATH.
Section 2. Setting up and running the program
2.1. How to do a reducing run?
A reducing run removes unoccupied conformers so that the dieletric boundary will
be more accurate in delphi calculations. Run "reduce_conf.py" will print out a
reduced pdb file in step2_out.pdb format. Run "reduce_conf.py > step2_out.pdb" will replace the existing step2_out.pdb file. Then you need to rerun step3 and step4 only.
Section 3. Understanding MCCE
3.1. What is "hydrogen bond directed rotamer making"?
This is an advanced feature of rotamer making step. Usually, the rotamer
packing is performed with Van de Waals potential only. When this option is on,
a hydrogen bond energy term will be considered in rotamer tuning and packing.
Non-polar residues remain unaffected.
3.2. How is "hydrogen bond directed rotamer making" implemented?
Step 1, a progressive "swing" is performed to "attract" conformer pairs with
O-O and O-N distances between 2.5 and 3.5 A to the distance 3.0 A, which is more
likly to be hydrogen bond distance. This step creates hundreds to thousands of
conformers on each polar/ionizable residues.
Step 2, one conformer with the O-O/O-N distance closest to 3.0 will be elected
from a set conformers within a distance threshold. This reduces one third of the
conformers at distance threshold of 0.5 A without losing representivity.
Step 3, the conformers are sorted with the recorded distance to its potential
hydrogen bond partner. The first 100 conformers (or other predefined numbers) with
the distances closest to 3.0 A are seletect.
Step 4, all residues go to repacking with hydrongen bond energy on.
3.3. How to interprete conformer history in step2_out.pdb and step3_out.pdb?
The conformer history is a 10-character string.
The first two describes the conformer type as in tpl file.
The next 4 characters indicate how the the heavy atom rotamer was made. "____" is for backbone and never appers in fort.38, sum_crg.out, and head3.lst. "O000" is
for the native heavy atom conformer, "R###" (# is a digital number) is for rotated
conformers, and "H###" is for hydrogen bond directed rotamers.
The last 4 characters are about how rotamers were further ralaxed by MD. The optimized
rotamer is not far away from its parent heavy atom rotamer.
3.4. Why did I get "pKa out off range" in the pKa report file pK.out?
That is because the MCCE totration curve fitting program is not able to find the midpoint of the curve. You can still get the ionization information from file "sum_crg.out" and "fort.38". To understand why the titration is out of range, try program mfe.py whose documentation is available from http://www.sci.ccny.cuny.edu/~jmao/mcce/tools.html.
3.5. What is "WARNING: Delphi failed at focusing depth ..." error?
This is a dephi error reported by MCCE. The root cause is the complex protein surface caused by multiple conformers. Sometimes rotating the protein will help. If it doesn't work, reduce the number of conformers by using quick run or default run.
Section 4. Tools
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