Re: [charmm-bbs] H-bond parameters (2)



Hi Lesley,
 I'm glad you asked these two questions, because they point out some
 important aspects I was trying to make in my earlier response.
 Empirical force fields can *only* calculate those energy term they are
 parameterized for, so if you are using a force-field that wasn't
 parameterized using an explicit H-Bond term, it would be an inappropriate
 question to ask "what is the H-Bond component".
 To ask this question, you'd have to use a force-field that was
 parameterized using explicit H-Bonding terms (which would no doubt
 have other parameters different [e.g. electrostatics and vdW])
 You can 'approximate' the strength of the H-Bonds by 'turning them on'
 (i.e. incr. cuthb) but these numbers should *not* be relied upon too
 greatly, since, again, those values were not used in the force-field
 optimization.  They are probably hold-overs from earlier optimizations
 when they were included explicitly.
 As for 'what do you do when there are no H-Bond terms in the force-field'
 (even if you are using a field that has explicit H-Bond terms); the answer
 there
 is the same as any 'missing parameter' problem, i.e. you'd need to search
 the literature to see if anyone has optimized such a parameter *using* the
 same force-field you are using.
 The script I provided still works with a Cys present, but you're right,
 since there are not terms to calculate, one cannot even analyze for
 H-Bond geometries (which is the recommended use of the H-Bond
 commands I gave; also Lennart Nilsson reminded us of the
 "coor hbond" command which helps with analysis w/o the use of
  the force-field parameters).
 DG
 At 04:25 PM 10/11/1999 +0100, you wrote:
 >Thank you all for your help regarding my recent question on H-bond
 >parameters. Following on from everything that has been said I would like
 >to ask two more questions:
 >
 >(1) If hydrogen bonding is implicit in electrostatics and vdW terms, how
 >do you analyse the energy term to find the contribution to energy which
 >is due to hydrogen bonding? I assume this is a valid occasion for using
 >HBONDS
 >
 >(2) If you determine the energy due to hydrogen bonds using HBONDS CUTHB
 >4.5 (for example), how do you account for sulfur containing systems,
 >particularly cysteine residues, when sulfur is not parameterised in the
 >HBOND section of the parameter file?
 >
 >If you run the script that Don Gregory sent to the list, but replace one
 >of the residues with CYS this adapted script falls over because there
 >are no hydrogen bond parameters.
 >
 >Thanks again for your help so far. Look forward to hearing from you
 >again.
 >Lesley
 Dr. Don Gregory (dgregory |-at-| msi.com)
 Asia Pacific Science Liaison
 Molecular Simulations Inc.
 9685 Scranton Rd.
 San Diego, CA  92121
 (619) 799-5331     http://www.msi.com