CHARMM Development Project
Posted By: mzzt Imporper Dihedral Parameter - 07/21/07 07:39 AM
Dear All,

I am trying to use PRES GLYQ patch in C27 and hence transferring the desired parameters for this patch from Charmm22 to Charmm27.
Everything else seems to be working fine except for an extra imporper dihedral parameter in charmm27. E.g. when I use C22 then it reports a total of 418 improper dihedral angles, and hence gets over without any error, whereas C27 reports one extra i.e. 419 imporper dihedral angles for the same protein.

The missing parameter is:

CC - CT1 - NTL - O

CC = carbonyl C of asn, asp, glu, gln, cter, ct2
CT1 = aliphatic sp3 C for CH
NTL = ammonium nitrogen
O = carbonyl oxygen

Now, How should I incorporate this parameter. Will it be right to add the values of

X CT1 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL
! 0.715->0.10 METHYLAMMONIUM (KK)

for my missing parameter(X CT1 NTL X), since they appear to be close.

Kindly suggest me something,
Eagerly waiting for the charmmers response,
Posted By: mzzt Re: Improper Dihedral Parameter - 07/27/07 01:26 PM
Dear All,

This problem occurs because the program tries to make a link between the protein and the first atom of the lipid bilayer.

So in order to solve this just generate the protein and bilayers separately and this missing parameter would no longer be a problem.

Hope this would be of help to others,

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