Hello, gods of gromacs, I have ported the parmbsc0 modifications to a new gromacs force field, based on the amber99sb.ff, this involves adding a new carbon atom (CI) to be used in the C5' of nucleotides.
Everything is working perfectly (to my astonishment) and I am confident of all of the modifications I have made, except for the func column in [diheadraltypes]. The only way I can get the parameters that involve the same four atoms to work is to alter this column. I have read chapter 5 but I cannot see in what way this will affect the new ff. These are the original parameters from AMBERparmbsc0: DIHE X -CI-OS-X 3 1.150 0.0 3.0 X -CI-OH-X 3 0.500 0.0 3.0 X -CI-CT-X 9 1.400 0.0 3.0 CT-OS-CT-CI 1 0.383 0.0 -3.0 CT-OS-CT-CI 1 0.100 180.0 2.0 H1-CI-CT-OS 1 0.250 0.0 1.0 H1-CI-CT-OH 1 0.250 0.0 1.0 H1-CT-CI-OS 1 0.250 0.0 1.0 H1-CT-CI-OH 1 0.250 0.0 1.0 CI-CT-CT-CT 1 0.180 0.0 -3.0 CI-CT-CT-CT 1 0.250 180.0 -2.0 CI-CT-CT-CT 1 0.200 180.0 1.0 OS-P -OS-CI 1 0.185181 31.79508 -1.0 alfa OS-P -OS-CI 1 1.256531 351.95960 -2.0 alfa OS-P -OS-CI 1 0.354858 357.24748 3.0 alfa OH-P -OS-CI 1 0.185181 31.79508 -1.0 alfa OH-P -OS-CI 1 1.256531 351.95960 -2.0 alfa OH-P -OS-CI 1 0.354858 357.24748 3.0 alfa CT-CT-CI-OS 1 1.178040 190.97653 -1.0 gamma CT-CT-CI-OS 1 0.092102 295.63279 -2.0 gamma CT-CT-CI-OS 1 0.962830 348.09535 3.0 gamma CT-CT-CI-OH 1 1.178040 190.97653 -1.0 gamma CT-CT-CI-OH 1 0.092102 295.63279 -2.0 gamma CT-CT-CI-OH 1 0.962830 348.09535 3.0 gamma This is from my amberbsc0/ffbonded.itp: ;i j k l func phase kd pn CT OS CT CI 4 0.00 0.38300 -3 ; parmbsc0 ----> Will Stebbeds CT OS CT CI 4 180.00 0.10000 2 ; parmbsc0 ----> Will Stebbeds H1 CI CT OS 4 0.00 0.25000 1 ; parmbsc0 ----> Will Stebbeds H1 CI CT OH 4 0.00 0.25000 1 ; parmbsc0 ----> Will Stebbeds H1 CT CI OH 4 0.00 0.25000 1 ; parmbsc0 ----> Will Stebbeds CI CT CT CT 4 0.00 0.18000 -3 ; parmbsc0 ----> Will Stebbeds CI CT CT CT 4 180.00 0.25000 -2 ; parmbsc0 ----> Will Stebbeds CI CT CT CT 4 180.00 0.20000 1 ; parmbsc0 ----> Will Stebbeds OS P OS CI 4 31.79 0.18518 -1 ; parmbsc0 ----> Will Stebbeds OS P OS CI 4 351.96 1.25653 -2 ; parmbsc0 ----> Will Stebbeds OS P OS CI 4 357.25 0.35486 3 ; parmbsc0 ----> Will Stebbeds OH P OS CI 4 31.79 0.18518 -1 ; parmbsc0 ----> Will Stebbeds OH P OS CI 4 351.96 1.25653 -2 ; parmbsc0 ----> Will Stebbeds OH P OS CI 4 357.25 0.35486 3 ; parmbsc0 ----> Will Stebbeds CT CT CI OS 4 190.98 1.17804 -1 ; parmbsc0 ----> Will Stebbeds CT CT CI OS 4 295.63 0.09210 -2 ; parmbsc0 ----> Will Stebbeds CT CT CI OS 4 348.09 0.96283 3 ; parmbsc0 ----> Will Stebbeds CT CT CI OH 4 190.98 1.17804 -1 ; parmbsc0 ----> Will Stebbeds CT CT CI OH 4 295.63 0.09210 -2 ; parmbsc0 ----> Will Stebbeds CT CT CI OH 4 348.10 0.96283 3 ; parmbsc0 ----> Will Stebbeds ;i j k l func X CI OS X 9 0.0 1.15000 3 ; parmbsc0 ----> Will Stebbeds X CI OH X 9 0.0 0.50000 3 ; parmbsc0 ----> Will Stebbeds X CI CT X 9 0.0 1.40000 3 ; PARMBSC0 ---> Will Stebbeds As you can see func=1 was changed to func=4 and func=3 was changed to func=9. This was the only way I could find in which the parameters would work, is it valid to make such alterations arbitrarily? The only other way it will work is if I comment out the repeated lines for the same 4 atoms. Any help on this matter would be very much appreciated. best regards Will > Date: Sat, 5 Feb 2011 12:23:32 -0500 > From: [email protected] > To: [email protected] > Subject: Re: [gmx-users] Porting Amber parmbsc0 force field to Gromacs > > > > william Stebbeds wrote: > > Hello, > > > > I would like to use the parmbs0 Amber forcefield to Gromacs, > > specifically the nucleic acid parameters. > > > > Is this likely to come in a future release? > > > > Force fields are only implemented if a developer has a compelling reason to > do > so, and then take the time to validate it. As such, new force fields are not > often introduced. > > > I appreciate that this will likely be a difficult process but if anyone > > can point me in the right direction I would be very grateful. > > > > You can probably take an existing Amber force field and modify it. Chapter 5 > is > your friend here. By modifying existing files, you don't have to come up > with > all the syntax by yourself. > > -Justin > > > Will - Cranfield University > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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