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create alanine dipeptide what to use when ACE or ACED
#38069 08/26/20 10:33 AM
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Rohit Offline OP
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Hello,

In top_all36_prot.rtf file there are 2 patches ACE and ACED. it says do not use ACE for dipeptides.

I want to create N–acetyl–N′–methyl–L–alanylamide also called as alanine dipeptide. (ACE-ALA-NME).

I want to know what are the difference between the 2 patches ACE and ACED. which one should I use to create alanine dipeptide and why not the other patch.

I dont see the difference other than in the CMAP where ACE has N+ and ACED has NT.

Thank-you,
Regards,
Rohit Modee

Last edited by Rohit; 08/26/20 10:34 AM.
Re: create alanine dipeptide what to use when ACE or ACED
Rohit #38070 08/26/20 03:39 PM
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rmv Offline
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You can use the whole molecule definitions in stream/prot/toppar_all36_prot_model.str either ALAD or ALAC (w. CMAP)


Rick Venable
computational chemist


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