[gmx-users] dna topology in OPLS force field

[Justin Lemkul]

On 2/2/16 11:53 AM, soumadwip ghosh wrote:
> Hello,
>          I am facing some difficulty to simulate single stranded DNA and a
> single walled acrbon nanotube. I need different CNTs (with various m and n)
> for my study and I am generating them using g_x2top accoring to Andrea
> Mineoi's tutorial. It seems to be ok. On the other hand I have to make
> topology for ssDNA which I am finding very difficult to generate using OPLS
> force field. I tried Topolgen and Topolbuilder both but in the output
> topology atomtypes are not defined and the net charge comes out to be zero
> which should be -11. My question is is there a possible way to generate
> CNTs in combination with CHARMM27 force field with pdb2gmx with all the
> dihedral and angle parameters unambiguously. I guess I cannot use g_x2top
> in connection with CHARMM. Or is there a way to convert the cnt.top I have

That's not correct; you can use x2top with any force field, you just have to 
write a .n2t file.

> (the OPLS one) into CHARMM atomtypes and parameters? I would appreciate any
> insight in this regard. Sorry for asking much.
>

In principle, a CNT is just the same atom type over and over again (unless 
you've got capping groups on the end) and a few bonded parameters.  It should be 
very simple to write a topology.  Whether or not this representation is adequate 
to describe the physics is another matter.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================