[gmx-users] Charmm27 and Charmm36 atomtypes assignments for polymer

[Justin Lemkul]

On 11/19/19 9:54 PM, Mijiddorj B wrote:
> Dear Gmx users,
>
> Currently, I am trying to assign the atomtypes in charmm27 for the
> polyethyleneimine polymer. It includes several different groups of atoms. I
> included following illustration and asignment:
> ##############################################
>                           H                     CH2
>                           |                     /
> NH2--CH2--CH2--N--CH2--CH2--N--CH2 ...
>
> ##############################################
> I assigned and the charmm27 atomtypes as following and compared charmm36
> atomtypes generated by CgenFF.
> Atom       Charmm27     Charmm36
> N (NH2) ---> NH2       |    NG321
> N (NH1) ---> NH1       |    NG311
> C (CH2) ---> CT2       |    CG321
> H (HC2) ---> HA         |    HGA2
> N                 ?           |    NG301
>
> If you have any experience, please check my assignments the charmm27 atom
> types and advice me the atomtype of the last Nitrogen, which were assigned
> as NG301 with CgenFF.

Why are you replacing the CGenFF atom types? The replacements you are 
making completely change the LJ terms and therefore render the dihedral 
parameters invalid. There is no need to make these changes, just use the 
CGenFF atom types in your simulation (all of which is contained in the 
CHARMM36 port, which you should use rather than the outdated CHARMM27 
force field files).

-Justin

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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