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: Fri Jul 18 2008 - 07:08:48 CDT

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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