AMBER Archive (2008)

Subject: AMBER: Hydroxyprolines!!!

From: Titus, Jamie \(bairdje\) (BAIRDJE_at_ucmail.uc.edu)
Date: Wed May 07 2008 - 13:54:03 CDT

Hello all,

I having been running a simulation of a protein in complex with CRP(collagen-like peptide) using the hydroxyproline forcefield parameters available on https://simtk.org/home/hydroxyproline. I believe I may have any issue calculating surface areas using gbsa, though. (correct me if I am wrong, please). I saw in a previous post(http://amber.ch.ic.ac.uk/archive/200704/0151.html) that modifying the mdread.f file in src/sander(would you need to modify mdread.f in any other folder, too?) was recommended. The hydroxyproline forcefield parameters use the atom type 'OO' which I do not see in the mdread.f file. Will I need to add this atom type to this file to be able to calculate surface areas of molecules containing hydroxyproline? Is there more that will be required?

This is how I would modify the file (a total guess)(...a section from the oxygen section of the file):
            else if (atype == 'O ') then
               x(l165-1+i) = 1.60d0 + 1.4d0
               x(l170-1+i) = 0.68563d0
               x(l175-1+i) = -0.1868d0
               x(l180-1+i) = -0.00135573d0
               x(l185-1+i) = 0.00023743d0
            else if (atype == 'O2') then
               x(l165-1+i) = 1.60d0 + 1.4d0
               x(l170-1+i) = 0.88857d0
               x(l175-1+i) = -0.33421d0
               x(l180-1+i) = -0.0018683d0
               x(l185-1+i) = 0.00049372d0
            else if (atype(1:1) == 'O' .or. atype(1:1) == 'o') then
               if (nbond == 1) then
                  x(l165-1+i) = 1.60d0 + 1.4d0
                  x(l170-1+i) = 0.77914d0
                  x(l175-1+i) = -0.25262d0
                  x(l180-1+i) = -0.0016056d0
                  x(l185-1+i) = 0.00035071d0
               else if (nbond == 2) then
                  x(l165-1+i) = 1.60d0 + 1.4d0
                  x(l170-1+i) = 0.49392d0
                  x(l175-1+i) = -0.16038d0
                  x(l180-1+i) = -0.00015512d0
                  x(l185-1+i) = 0.00016453d0
            else if (atype == 'OO') then
               if (nbond == 1) then
                  x(l165-1+i) = 1.60d0 + 1.4d0
                  x(l170-1+i) = 0.77914d0
                  x(l175-1+i) = -0.25262d0
                  x(l180-1+i) = -0.0016056d0
                  x(l185-1+i) = 0.00035071d0
               else if (nbond == 2) then
                  x(l165-1+i) = 1.60d0 + 1.4d0
                  x(l170-1+i) = 0.49392d0
                  x(l175-1+i) = -0.16038d0
                  x(l180-1+i) = -0.00015512d0
                  x(l185-1+i) = 0.00016453d0
               end if

tried naccess - there are no parameters for hydroxyproline surface area that I can find on the web or in references.
again - running serial amber9 on linux amd opteron dualcore. Thanks!

Jamie Baird-Titus
Post-Doctoral Fellow
Laboratory of Professor Mark Rance
Department of Molecular Genetics, Biochemistry, and Microbiology
University of Cincinnati College of Medicine
Rm. 3109 Medical Sciences Bldg.,
231 Albert Sabin Way, Cincinnati, OH 45267
phone:(513)558-2938
email:bairdje_at_ucmail.uc.edu
website: http://jamiebairdtitus.googlepages.com

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