[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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