Re: AMBER: Angle parameters in phosphate groups

From: Seongeun Yang <>
Date: Sat, 14 Aug 2004 18:58:07 +0900

Thanks for your curiosity.

I tried test simulations of ACE-SEP(-1)-NME and ACE-SEP(-2)-NME,
as you suggested.
The md simulation procedure is as follows:
1. minimization of solute with constrained solvent
    minimization of solvent with constrained solute
    minimization of the total system
2. heating from 0 to 500 K
3. production run at 500 K

The input parameters are the same for both species.
The atomic partial charges were calculated using antechamber.
Except for these charges, all the other parameters come from parm99.dat

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.


----- Original Message -----
From: "Guanglei Cui" <>
To: <>
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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Received on Mon Aug 16 2004 - 09:53:01 PDT
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