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topology and parameter file for neutral amino acid
#34922 04/14/15 04:26 AM
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akshay Offline OP
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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.


Last edited by akshay; 04/14/15 04:33 AM.
Re: topology and parameter file for neutral amino acid
akshay #34923 04/14/15 06:29 AM
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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.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: topology and parameter file for neutral amino acid
akshay #37075 07/26/18 12:56 PM
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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.

Re: topology and parameter file for neutral amino acid
akshay #37076 07/26/18 05:06 PM
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rmv Online Content
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You search was incomplete, and apparently did not include the files in the stream/prot subdirectory.


Rick Venable
computational chemist

Re: topology and parameter file for neutral amino acid
akshay #37079 07/28/18 05:05 AM
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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).

Re: topology and parameter file for neutral amino acid
akshay #37080 07/28/18 11:34 PM
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rmv Online Content
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(1) patches CNEU and NNEU in top_all36_prot.rtf
(2) patches in stream/prot/toppar_all36_prot_arg0.str


Rick Venable
computational chemist


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