RE: AMBER: how to generate psf file using the AMBER topology file

From: Ross Walker <ross.rosswalker.co.uk>
Date: Fri, 18 Jul 2008 09:57:14 -0700

Hi Madhurima,

 

That should probably read - "format used in AMBER 6 or the new format first
defined in AMBER 7 and used in subsequent versions of AMBER".

 

And AMBER 9 prmtop file is the same format as was introduced in AMBER 7.

 

If you are using AMBER in NAMD I would suggest that you make sure you set
the 1-4 electrostatic and 1-4 VDW scaling correctly, since the default in
NAMD is 1.0 which is for the CHARMM force fields, not AMBER. Although this
will still cause you problems because the GLYCAM 06 force field requires 1.0
scaling while the FF9X force fields require 1.2. Currently neither code
supports a combination of the two - but work is in progress on AMBER to
address this.

 

Also I would check very carefully that you get the same results in AMBER and
NAMD. I.e. run about 10 steps of MD and make sure you that you know how to
set the options up correctly that you can get the same results (to around 3
decimal places or so) in both codes.

 

All the best

Ross

 

From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
tinni sona
Sent: Friday, July 18, 2008 5:09 AM
To: amber.scripps.edu
Subject: Re: AMBER: how to generate psf file using the AMBER topology file

 

Hi,

Thank you very much for the reply. I have an another question that if NAMD
is able to read the directly prepared amber topology and inpcrd files
generated from AMBER9? Here in NAMD manual it is given "NAMD can read PARM
files in either the format used in AMBER 6 or the new format defined in
AMBER 7."

regards,
Madhurima



On Fri, Jul 18, 2008 at 4:39 PM, Balazs JOJART <jojartb.pharm.u-szeged.hu>
wrote:

Hello,
NAMD is able to read directly the prepared amber topology and inpcrd files.
for example:
amber on
parmfile ***.parm7
ambercoor ***.inpcrd or ***.rst
hope this helps.
balazs



tinni sona wrote:

Hi All,

I want to perform the MD simulation of protein-carbohydrate complex using
NAMD. My force field is AMBER. I'm failed to generate the required psf file
for the system using the AMBER and GLYCAM topology files for protein and
carbohydrate respectively.

Can anyone please suggest me how to generate the psf file using topology
file taken from AMBER?
I would really appreciate if you could respond.

Thanks,
Madhurima

 

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Received on Sun Jul 20 2008 - 06:07:44 PDT
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