[gmx-users] Creating a chain of homo polymer from a non standard residue

[Janakiraman Balachandran]

Hi,

My challenge is in creating polymer chain input for Gromacs. For example if
I have a manually created PDB file of a single non-standard residue of
repeat unit of polyethylene glycol (CH2-O-CH2) as given below.
I have used this pdb file in `x2top` to create a corresponding rtp file

My question is, what software can I use that --
*(i) reads this non-standard residue in PDB format and *
*(ii) Creates a homo polymer chain of arbitrary size (n)  and writes the
output into a format (ex: pdb) that can be then used in `pdb2gmx` to create
a `.gro` for the MD simulation.*


*PDB File for repeating residue:*

REMARK   Materials Studio PDB file
REMARK   Created:  Mon Dec 04 09:52:49  2017
ATOM      1  CT1 EGR H   1     -14.882   2.339   0.134  1.00  0.00
 C
ATOM      2 HC11 EGR H   1     -14.677   2.559   1.234  1.00  0.00
 H
ATOM      3 HC12 EGR H   1     -14.774   3.298  -0.472  1.00  0.00
 H
ATOM      4  OS1 EGR H   1     -13.892   1.317  -0.371  1.00  0.00
 O
ATOM      5  CT2 EGR H   1     -12.493   1.852  -0.184  1.00  0.00
 C
ATOM      6 HC21 EGR H   1     -12.292   2.009   0.928  1.00  0.00
 H
ATOM      7 HC22 EGR H   1     -12.392   2.846  -0.732  1.00  0.00
 H
TER       8
CONECT    1    2    3    4
CONECT    2    1
CONECT    3    1
CONECT    4    1    5
CONECT    5    4    7    8    6
CONECT    6    5
CONECT    7    5
END