Re: AMBER: using glycam04 parameters

From: <>
Date: Thu, 19 Apr 2007 19:53:37 +0200

Hi Sara,

        Your original question came up a while ago, and was answered on this

        To answer your latest question, I would advise you doing the
tutorials found on the Amber9 website to gain an understanding of how
Amber works - what files are used, when they are used, and what role
do they play in your job. If you have done the tutorials already,
then read through the leaprc file and see what it tells you. You will
notice that this file references the Glycam prep (filename.prep) file
and the Glycam parameter files (ie. filename.dat), as well as a few
other things.

        Amber is not a "black box." In order to use the program effectively
you have to make sure you understand what the program is doing. After
years of using this program, I am still learning new things almost
every time I use it :) .

Best of luck,

P.S. In response to Francois' suggestion about borrowing parameters
from another force field. This has to be done with caution. The
recent versions of Glycam (04-06) was developed using unity scaling
factors (ie. SCEE=SCNB=1). This is in contrast to how the other
Amber force fields are developed. Mixing parameters from different
force fields is likely to introduce artifacts into the calculations,
whose severity is not known. Ideally, one might benchmark the
"frankensteined" force field on a small test set of compounds, much
like is done during force field development. This can be time
consuming and doing so could be weighed with how "important" that
particular parameter might be in your simulation.

On 19.04.2007, at 18:27, Sara Alexandra Moura wrote:

> I've dowloaded Glycam_04.prep, Glycam_04l.dat e leaprc.Glycam_04.
> In which
> folders do I have to save the files in order for them to work?
> Thank you!
> Sara Alexandra Moura

> From: "Austin B. Yongye" <>
> Date: 18. April 2007 18:03:35 MESZ
> To:
> Subject: Re: AMBER: using glycam04 parameters
> Reply-To:
>> I have used that site, but I need to use Xleap to solvate the
>> system, and
>> it does not recognize the C1-OH, even when created by that site.
> You can get the .top/.crd files,etc from The site also
> gives you the option of solvating your system. Anyway, if you are
> going to
> solvate the system using x/tleap, you need the parameter and prep
> files on
> your local machine. So, did you download the latest parameters and
> prepfiles?
> You can post your leap input files, so we know what your are doing.
> Austin-

> I have tried "source leaprc.glycam04" or loading it when I
> initialize xleap.
> I've saved the parameters file 1GB as a PDB and it has no OH at C1
> and no H
> either! So where are the missing parameters?!
> Thank you.
> Sara Alexandra Moura

> I have used that site, but I need to use Xleap to solvate the
> system, and it
> does not recognize the C1-OH, even when created by that site. What
> is the point
> of having a carbohydrates parameters set, if I have to compute
> parameters for
> the C1-OH linkage, it makes no sense!
> I'm really frustrated...
> Thank you!
> Sara Alexandra Moura

> You can download the latest glycam04 parameters, and prepfiles from
> this
> website:
> Also check out this link:
> option=glycam04&option2=FF94
> You will be able to build the glycans you want, and
> download .top/.crd and
> leap input files.
> Austin-

>> How can I use the parameters for beta-glucose? Xleap always tels
>> me the
>> parameters for the C1-OH linkage are missing and it does not
>> recognize the
>> OH...
> I wonder if the FF parameters for hemiacetals are in GLYCAM FF. It
> might have only FF parameters for Methyl-glycoside derivatives...
> In this case, just pick up the missing FF parameter from GAFF for
> instance, or compute your own FF parameter.
> regards, Francois
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Received on Sun Apr 22 2007 - 06:07:32 PDT
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