On Mon, Apr 23, 2012, 本人 wrote:
> 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?
There are two separate issues here:
1. Should you use Amber atom types or GAFF atom types for your modified
nucleotides? There is no "correct" answer, but if the modification from
standard nucleotides is small, using amber types is likely to be the better
route. Please look at examples, either at the Wayne State site, or at the
contributed parameters database (both are linked from the Amber web page.)
2. How to use antchamber for modified residues, rather than for "complete
molecules": this is discussed in the "residuegen" routine of antechamber
(section 4.4.3 of the AmberTools12 Reference Manual, similar places in earlier
manuals). Warning: I've not used this program, and you may have to experiment
a bit. Send email to Junmei Wang (junmwang.yahoo.com) with questions, since
he generally does not follow this mailing list.
>
> > 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.
This is a completely separate problem. Without knowing what is in the
aa.frcmod file, it is hard to say what is going on.
....dac
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Received on Mon Apr 23 2012 - 10:00:03 PDT
