paulrobustelli / force-fields Goto Github PK

Hi there,

I am finding this AA99SB-disp FF pretty interesting and I wanted to use it in a NAMD simulation. I am fairly new to MD and was wondering if anyone could point me in the right direction - I'd love all the help I can get!

Cheers

Missing Improper Dih. types

CT CC CW NA

which is used for HIS.

Hello,

I'm trying to use the 99SB-disp in amber20. I've copied the files into their respective directories as instructed. I run tleap:

source leaprc.protein.ff99SBdisp
source leaprc.water.tip4pd_disp

and I am able to solvate with TIP4PDBOX. However when it comes to saving the parameter and coordinate files I get errors:

Error: For atom (.R<WAT 4401>.A<H2 3>) could not find vdW (or other) parameters for type (HW)

I downloaded the git several days before so I still have the parm99.dat file that was recently removed. When I compare this file to the parm99.dat in amber20/dat/leap/parm I notice that the amber20 version does not include parameters for HW and OW which are in the parm99.dat file that was included previously. If I have that parm99.dat file in my working directory, it works as expected.

Would an acceptable solution be to source leaprc.water.tip3p before sourcing the tip4pd_disp file?

Thank you,
Kari Gaalswyk

There is some empty space in the reference water a99SBdisp_water.gro structure file of the a99SBdisp FF. This empty space also translates into solvated simulation boxes. Is that intended?
Best,
Soeren

I'm planning to simulate some proteins using the a99sb-disp ff. To set up my system, I used Gromacs with the Gromacs ff provided in this repo. I obtained .top files that are compatible with both Gromacs and openmm. However, for some reasons, I need to use openmm. To ensure that openmm runs correctly, I calculated the potential of my initial structure using both openmm and Gromacs. Surprisingly, I discovered that these two produced different potentials. The difference came from non-bonded potential. After delving into the Gromacs ff files and conducting experiments with toy systems, I identified two factors contributing to this inconsistency.

1. In the file Gromacs_FFs/a99SBdisp.ff/a99SBdisp_water.itp, the [bond] and [angle] sections were missing. The absence of the [bond] caused openmm to produce incorrect potential for rigid water. When I compared the Gromacs and openmm potential energies for a pure water system, I observed a difference of 200 kJ/mol (approximately 0.1%). This discrepancy was about ten times larger than what I typically observed with other ff. I added [bond] and [angle] sections based on those found in the tip4p water model. After this adjustment, the difference for the pure water system decreased to about 0.01%, which is more reasonable.

2. In the file Gromacs_FFs/a99SBdisp.ff/ffnonbonded.itp, there is a [nonbond_params] section after the [atomtype] section. This section was overriding the non-bonded parameters for HB and OB pairs that should be calculated based on combination rules. The presence of this section caused openmm to produce potential that were 100% higher than expected for a toy protein system. Removing this section resulted in a perfect potential matching. However, I believe we should keep it. It may be a bug with openmm. But I think it is still necessary to mention it here in case someone has the similar issue .

(BTW, I also compared openmm potential and amber potential using an amber format a99sb-disp ff. I also obeserved different potential. This difference is from dihedrals. I am not familiar with amber so I didn't spend time to fix it)

Ion parameters in the gromacs port of 99sb-disp (in ffnonbonded.itp) appear to be of the Aqvist type rather than charmm22

Hi Paul,

For a threonine at the N terminus (NTHR), angle types N3 CT C8 and HP CT C8 are missing. This could be coming from the fact that you have CB bonded to C8 ( line 2814 in aminoacids.rtp) as opposed to CB bonded to CT in amber99SB. Was there a mistake in copying the structure perhaps? Or maybe the parameters missing?

Thanks!

The ions.itp files with the [ moleculetype ] definitions of the ions are missing in the des-amber directories for Gromacs.

Hi All,
I'm trying to use the ff99SBdisp force fields with Amber20. All relevant files from GitHub have been copied to the cmd, lib and parm directories of the Amber installation tree.
However, when I try to load the leaprc files tleap crashes with a syntax error:
`> source leaprc.protein.ff99SBdisp
----- Source: /home/gard/Code/amber20_src/dat/leap/cmd/leaprc.protein.ff99SBdisp
----- Source of /home/gard/Code/amber20_src/dat/leap/cmd/leaprc.protein.ff99SBdisp done

/home/gard/Code/amber20_src/bin/teLeap: Fatal Error!
Error from the parser: syntax error

Exiting LEaP: Errors = 1; Warnings = 0; Notes = 0.
`

The same happens when loading leaprc.water.tip4pd_disp. Tleap doesn't write any logs with additional information. Can you think of a possible reason for this?

Thank you in advance

Sasha

In des-amber-SF1.0.ff/ the mass of Vrt atom is 1, while in des-amber.ff/ it's 0. Is that correct?