CHARMM Development Project Forums User Discussion & Questions Setup, I/O, and Basic questions create alanine dipeptide what to use when ACE or ACED

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

You can use the whole molecule definitions in stream/prot/toppar_all36_prot_model.str either ALAD or ALAC (w. CMAP)