[gmx-users] Porting Amber parmbsc0 force field to Gromacs
william Stebbeds
willstebbeds at hotmail.com
Mon Feb 21 14:49:02 CET 2011
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: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> 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
>
> ========================================
> --
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