[gmx-users] Rtp for polymer.

Andrea Muntean andreamuntean at gmail.com
Thu Feb 5 09:39:38 CET 2009

I connect the monomers by adding a bond in the rtp entry, in which the
first atom of the next residue is given with + (you can also connect
with the previous residue with - in front of the last atom). Sorry to
explain this in a very confuse way. Better look at the example bellow
(for polystyrene):

CH2     CH2     0       0
CH      CH1     0       0
CB      C       0       0
CG1     CR1     0       0
CG2     CR1     0       0
CG3     CR1     0       0
CG4     CR1     0       0
CG5     CR1     0       0

;-CH    CH2     gb_ (you put the appropriate bond from the ff*_bon.itp file)
CH2     CH      gb_
CH      CB      gb_
CB      CG1     gb_
CG1     CG2     gb_
CG2     CG3     gb_
CG3     CG4     gb_
CG4     CG5     gb_
CG5     CB      gb_
CH      +CH2    gb_

(angles, impropers and dihedrals were defined accordingly, but not listed here)

I hope that will help.

2009/2/5 varsha gautham <varsha.gautham88 at gmail.com>:
> Hello  justin,
> Am sorry to say that its not useful.But what i mean is that the rtp
> constructed manually is building up the polymer and generating topology
> files and gro files.
> But when i look into the gro file with vmd the connectivity between each of
> the monomer is not built.That is my polymer consists of 10 monomer units
> with ben and primary amine unit as a block polymer.
> How can i include the connectivity information between these two in a rtp
> file?I can include that in session called bonds. But how to do that??And i
> want some help
> regarding the workflow that is how gromacs interpreting each of the rtp, atp
> ,ffnb.itp,ffbon.itp??I want to know that in a sequential order.are there any
> materials available other than manual..If so please let me know
> Thanks in advance.
> -krithika
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