CHARMM Development Project Forums User Discussion & Questions Parameter Set Discussion topology and parameter file for neutral amino acid

Dear all

I am trying to simulate a neutral (not in zwitter ion form) asparatic acid in water. The structure is:

COOH
|
CH2
|
COOH-C-NH2
|
H

But, in the topology and parameter files the details are there only for zwitter ion form. From where i can obtain the Charmm topology and parameter file for the above mentioned molecule.

This form does not really exist. If you could cap the termini with neutral groups there are a couple of possibilities available in top_all36_prot.rtf, also for the protonated Asp side chain. If you insist on the form you show, you have to make up the parameters yourself.

Hello everyone, I need to model neutral arginine (i.e. protonated H should not be with NH group) , But could not find any thing in charmm 36 force field for that. Any help is highly appreciated. Thanks in advance.

You search was incomplete, and apparently did not include the files in the stream/prot subdirectory.

Hello everyone, I need to model neutral arginine (i.e. protonated H should not be with NH group) , But could not find any thing in charmm 36 force field for that. Any help is highly appreciated. Thanks in advance.
Description:(1) COO- and NH3+ should be COOH and NH2
(2) Generally Arginine remains in protonated form but I want to make neutral Arginine in which among three nitrogen in biguanidine group should contain hydrogen in such a way that it be neutral as a whole (i.e. one less hydrogen than protonated form).

(1) patches CNEU and NNEU in top_all36_prot.rtf
(2) patches in stream/prot/toppar_all36_prot_arg0.str