CHARMM FF LONEPAIR

[Jumin Lee]

Dear OpenMM developers,

It seems like that current OpenMM only supports 'relative' and 'bisector' types of LONEPAIR for Drude FF.
Do you have any plan to implement the support of 'COLINEAR' type LONEPAIR for CGenFF?

Best,
Jumin

[Peter Eastman]

The LocalCoordinatesSite class is very flexible. It should be able to support any kind of lone pair used in CHARMM and many others. See http://docs.openmm.org/latest/userguide ... tual-sites.

Or are you talking about the implementation of the Drude force field in charmm_polar_2013.xml? If so, are you saying there are residues that are missing lone pairs? Which ones?

[Jumin Lee]

Sorry for confusing you.
No, I am talking about CHARMM PSF parser.

In wrappers/python/simtk/openmm/app/charmmpsffile.py line 374:
https://github.com/pandegroup/openmm/bl ... le.py#L374

Code: Select all

        if numlp != 0 or numlph != 0:
            lp_distance_list=[]
            lp_angle_list=[]
            lp_dihe_list=[]
            for i in range(numlp):
                lpline = holder[i].split()
                if len(lpline)!=6 or lpline[0] != '3' or lpline[2] != 'F' or int(lpline[1]) != 4*i+1 :
                    raise CharmmPSFError('Lonepair format error')
                else:
                    lp_distance_list.append(float(lpline[3]))
                    lp_angle_list.append(float(lpline[4]))
                    lp_dihe_list.append(float(lpline[5]))

COLINEAR type LONEPAIR only has 2 hosts so that lpline[0] is 2, and it does not have angle and dihedral terms.

[Peter Eastman]

I'm not familiar with that code. It was written by Jing Huang: https://github.com/pandegroup/openmm/pull/2120. Perhaps contact him and ask him about adding the other type?

[Jumin Lee]

OK. Thank you.
I will contact him.