AMBER Archive (2004)

Subject: Re: AMBER: Angle parameters in phosphate groups

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Sun Aug 15 2004 - 09:08:29 CDT

Hi, Seongeon

It'd be nice to have a few lines of your min output and other essential
files, such as parmtop and inpcrd, to see what's happened.

Seongeun Yang wrote:
> There was no error in assigning atom types in amber prep files.
> Each boxes were set to be neutral, of course, by adding Na+ ion(s).
> An error occurred while just minimizing ACE-SEP(-1)-NME.
> I checked the structure, minimized by around 200 steps, to be unreasonble.
> The O-H and other O in the phosphage group stuck together and formed
> almost a triangle.
>
> I don't think this error is from falsely assigned partial charges of phosphoserine.
> Because there was no problem in running a trajectory of the doubly charged
> phosphoserine capped with ACE and NME.
>
> Please give me an idea from where this error comes and take a look of angle
> parameters of OH-P-OS to compare between parm99.dat in amber
> and par_all27_prot_na.prm in charmm, if it's available.
>
> Thanks again.
>
> Seongeun
>
> ----- Original Message -----
> From: "Guanglei Cui" <cuigl_at_csb.sunysb.edu>
> To: <amber_at_scripps.edu>
> Sent: Thursday, August 12, 2004 11:18 PM
> Subject: Re: AMBER: Angle parameters in phosphate groups
>
>
>
>>Hi,
>>
>>I'm only curious about this. What would happen if you just built
>>phosphoserine with N- and C-caps and run the same procedure you
>>gave? It's hard to tell where the problem is with what you gave in
>>your email.
>>
>>Best,
>>
>>Guanglei
>>
>
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