AMBER Archive (2008)

Subject: Re: AMBER: how to generate psf file using the AMBER topology file

From: tinni sona (tinni.217_at_gmail.com)
Date: Sun Jul 20 2008 - 00:38:10 CDT

Hi,

Thanks to all of you for the valuable informations.

Now I'm using xleap to generate a combine force-field for
protein-carbohydrate complex. I'm using leaprc.ff03 and leaprc.GLYCAM_06 for
protein and carbohydrate respectively. But how will it be possible to use
these two at a time? Because if I use

#xleap -s -f leaprc.ff03
#list

only the protein residues are given.
and if

 #xleap -s -f leaprc.GLYCAM_06
#list

 only the residues for carbohydrates are displayed.

How shall i combine these two to generate the prmtop and inpcrd file for the
protein-carbohydrate complex?

Please suggest.
Thanks,
Madhurima

On Fri, Jul 18, 2008 at 10:27 PM, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> 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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *tinni sona
> *Sent:* Friday, July 18, 2008 5:09 AM
> *To:* amber_at_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_at_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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