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Posted By: mzzt PRES GLYQ - 07/10/07 06:58 AM
Dear all,

I wish to use GLYQ patch with CHARMM27 but it is not there in the topology file whereas it was there in the CHARMM22 topology file.
Is it correct to copy the PRES GLYQ parameters from CHARMM22 topology and paste it in the CHARMM27 top file?

Posted By: rmv Re: PRES GLYQ - 07/10/07 03:27 PM
As far as I know, except for the CMAP addition, protein parameters are "mostly C22"; the naming of the combined files (prot_na & prot_lipid) tends to blur that somewhat.
Posted By: mzzt Re: PRES GLYQ - 07/13/07 05:03 PM
Dear Prof. Venable,

Thank you so much for your reply.
I tried copying the following PRES GLYQ parameters from the C22 files into C27 file:

NTL CC 215.00 1.51 ! add by Simon Berneche

NH2 CT2 C 50.000 107.00 ! ALLOW PEP POL ARO ALI
! Simon Berneche 94/11/22 for PRES GLYQ for melittin from NH1 CT2 C 50.000 107.00

NH1 C CT2 NH2 0.6000 1 0.00 ! ALLOW PEP
! Simon Berneche for PRES GLYQ for melittin from NH1 C CT2 NH1 0.6000 1 0.00
O C CT2 NH2 0.0000 1 0.00 ! ALLOW PEP
! Simon Berneche for PRES GLYQ for melittin from O C CT2 NH1 0.0000 1 0.00
HC NH2 CT2 C 0.0000 1 0.00 ! ALLOW PEP
! Simon Berneche 94/11/22 for PRES GLYQ for melittin

in the parameter file and PRES GLYQ in the topology file. Still it gives me one missing parameter that is an improper dihedral angle: CC CT1 NTL O

What can I do about this? I am still not very sure of copying the parameters like this. Is this alright?

Posted By: rmv Re: PRES GLYQ - 07/13/07 06:50 PM
Great care must be taken to ensure that the appropriate atom parameters are being used under these kinds of circumstances. You should review the changes to make sure they make sense, and that the numbers are reasonable compared to similar types. Test the result.

I don't see PRES GLYQ in any of the distributed files; that could be someone's custom changes.
Posted By: mzzt Re: PRES GLYQ - 07/14/07 12:05 PM
Dear Prof. Venable,

I am carefully copying only those parameters which are specific for PRES GLYQ from the top and par files of C22. But this single missing parameter (improper dihedral angle) which I am getting even after that 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

This improper is linking my protein with the headgroup of lipid. Is this fine? I am not able to find any parameter which is close to this one in C22 as well as in C27.

Another point is suppose I wish to use GLYP and my protein doesnt have NH3+ and has only NH2 then can I add one extra hydrogen and use GLYP patch? (Shall I add this extra hydrogen using Hbuild??)

Posted By: mzzt Re: PRES GLYQ - 07/14/07 12:58 PM
Dear Prof. Venable,

This missing improper angle parameter error occur when I try to use the following:

imag byres sele resnam TIP3 .or. resnam DMPC end
update imall wmin 0.25 cutnb 3.0 ctonnb 3.0 ctofnb 3.0 cutim 3.0

(this is the last portion of sys8.inp file)

If I do not use this then I do not get this missing parameter.
Posted By: rmv Re: PRES GLYQ - 07/14/07 03:35 PM
If the UPDATE command does not succeed, then neither will any energy evaluations, including minimization or dynamics.

Improper torsions are used to maintain planarity, in this case of an amide, which seems to be very similar to the peptide backbone amide.

I don't understand the GLYP question; that should be the default N-term patch when Gly is the first residue. Using the NTER patch is incorrect for Gly. The GLYP patch will add two more H atoms to the PSF; you must then provide coords, ether from a file or possibly via HBUILD.
Posted By: mzzt Re: PRES GLYQ - 07/20/07 12:40 PM
Many thanks Prof. Venable.

I have found out that the above missing improper dihedral parameter is actually an extra parameter reported in C27. When I use C22 for the same file it reports eg. 418 improper dihedral angles whereas C27 reports 419 improper dihedral angles. Now, suppose I wish to switch off this extra improper dihedral, How would I do that? I tried to search for this parameter in the par file but not able to find it!!

Also, Will it be correct to add and modify
X CT1 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL
! 0.715->0.10 METHYLAMMONIUM (KK)

to X CT1 NTL X?

Kindly help,
Posted By: rmv Re: PRES GLYQ - 07/20/07 03:19 PM
Only the energy evaluation parameters (force constants and minima) are in the parameter file for improper dihedrals. Assigning improper torsions is not automated, and each one is explicitly defined in the topology file(s), for both RESIdues and PatchRESidues, via 'IMPR' statements.

I suggest the "Parameter Set" forum for the question on equivalent energy terms.
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