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 topology and parameter file for neutral amino acid
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Joined: Jan 2015
Posts: 3
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OP
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Joined: Jan 2015
Posts: 3 |
Dear all
I am trying to simulate a neutral (not in zwitter ion form) asparatic acid in water. The structure is:
COOH
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CH2
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COOH-C-NH2
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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.
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Re: topology and parameter file for neutral amino acid
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Joined: Sep 2003
Posts: 4,824 Likes: 2
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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
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Re: topology and parameter file for neutral amino acid
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Joined: Jul 2018
Posts: 3
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Joined: Jul 2018
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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.
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Re: topology and parameter file for neutral amino acid
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Joined: Sep 2003
Posts: 8,549 Likes: 3
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You search was incomplete, and apparently did not include the files in the stream/prot subdirectory.
Rick Venable
computational chemist
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Re: topology and parameter file for neutral amino acid
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Joined: Jul 2018
Posts: 3
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Joined: Jul 2018
Posts: 3 |
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).
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Re: topology and parameter file for neutral amino acid
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Joined: Sep 2003
Posts: 8,549 Likes: 3
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Joined: Sep 2003
Posts: 8,549 Likes: 3 |
(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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