Dear David:
Thanks for your advice, especially the website you tell me. however, my problem still exists, because my non-standard nucleotide was connected to
adjacent nucleotides, which means that this nucleotide cannot dealed with anchamber, for antechamber provides an automated method for creating non-standard units. However, it only works with complete molecules, not fragments as I have here. so what I am deeply confused is that the two different force fields , Do you mean I must use the only one force field (Amber99SB) here, for GAFF was only used for standalone molecular, and in other words "I can indeed mix GAFF and Amber99SB i.e. 2 different force fields ONLY when I have for instance a ligand and a protein i.e. NO CONNECTION between the ligand and the protein. and when I have a connection between two different parts I have to use the same force field" , am I right? But I don't know how to do it? can you tell me in detail?
Following your advice, when I added the missing terms to the frcmod file, FATAL error happenned, which may de due to the mixtion of two force field I used.
the error like this:
> loadamberparams aa.frcmod
Loading parameters: ./aa.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
!FATAL ERROR----------------------------------------
!FATAL: In file [varArray.c], line 182
!FATAL: Message: Realloc: Cannot allocate memory!
!ABORTING.
I'm hoping for your help, any advice would be appreciated!
zhangaidi
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Received on Wed Apr 25 2012 - 01:00:04 PDT
