Writing an amber force field which fits a branched polymer!

[Elsaid Mohamed]

I am developing an amber force field for a branched polymer, but so far it did not work.
I am looking for any source helping me to understand <HarmonicBondForce>,
<HarmonicAngleForce> and <PeriodicTorsionForce>.

Best,
Elsaid

[Peter Eastman]

Is there something specific you want to understand? If you're asking about the syntax of the XML file, that's described in http://docs.openmm.org/latest/userguide ... g_ffs.html. If you're asking about the functional forms of the different forces, see http://docs.openmm.org/latest/userguide ... orces.html.

[Elsaid Mohamed]

I successfully add the force block for a linear one, and it works. But I can not do a modified xml file to get the pdb file of the branched polymer get accepted by the program.
I think I have to understand deeply how bonds types are written there.

For that chain:(just an example )
(CHO2)(CH3)(CH3)
Every methy group is attached to an O from the first residue
I need to have an amber force field to the above (force blocks especially)
Thanks.

[Elsaid Mohamed]

What is the difference between the amber force field for linear and branched structures?

[Elsaid Mohamed]

The pdb file has 2 types of residues "COR and EGH" in 1 chain "A"
I define the residues like:
<Residue>
<Residue name="COR" >
C................
</Residue>
<Residue>
<Residue name="EGH" >
C................
</Residue>

Then I am getting the error:
anaconda3/envs/opki/lib/python3.10/site-packages/openmm/app/forcefield.py", line 295, in loadFile
resName = resname_prefix+residue.attrib['name']

KeyError: 'name'
there is something wrong?