From: Qiang Zhong (zqiang320_at_webmail.hzau.edu.cn)
Date: Tue Aug 21 2007 - 19:43:57 CDT
>From: Spiro Pavlopoulos <s.pavlopoulos_at_uconn.edu>
>Subject: namd-l: How to include parameters from stream files in calculations
>Date:Tue, 21 Aug 2007 16:02:39 -0400
>I am looking to do dynamics on peptides with phophorylated serines and am
> just trying to get to the point where I can run a minimization. After
> looking through the list I have succesfully used psfgen to construct the pdb
> and psf files by using top_all27_prot_na.rtf and toppar_prot_na_all.str .
> However when I try to run a simple minimization with NAMD using
> par_all27_prot_na.prm, it returns the following error.
> FATAL ERROR: CAN'T FIND BOND PARAMETERS FOR BOND CT2 - ON2 IN PARAMETER
> This is the bond between the CB of the serine sidechain and the oxygen of
> the phosphate group which apparently is not parameterized in
> If I have understood correctly from messages on the list, the stream file
> contains these parameters but I do not know how to make NAMD read these
> parameters from .str.
> I have tried adding the line
> parameters /toppar/stream/toppar_prot_na_all.str
you should copy the content(in final of file) about serine in
toppar_prot_na_all.str to the file par_all27_prot_na.prm.
> to the namd input file but it returns a message saying it cannot read
> the file.
> I would rather avoid cutting and pasting parameters from the .str to the
> .prm file. If someone could let me know the correct procedure or whether I
> am way off base I would greatly appreciate it.
> With Thanks
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:07 CST