Re: NAMD and new sugar parameter set

From: Rogan Carr (rogan_at_ks.uiuc.edu)
Date: Mon Apr 20 2009 - 18:43:58 CDT

Hi Gianluca,

You should be able to use psfgen as long as you have topology files
for your sugars (where the atoms are, what their charges/masses are
and how they are connected).

Cheers,
Rogan

On Apr 20, 2009, at 3:39 PM, Gianluca Interlandi wrote:

> Hi Rogan,
>
> Thanks for the answer. What about psfgen? I use CHARMM to create the
> PSF of the protein and then psfgen to solvate it. Does psfgen need
> to know about atom types?
>
> Gianluca
>
>
> On Mon, 20 Apr 2009, Rogan Carr wrote:
>
>> Hi Gianluca,
>>
>> I don't think it will be a problem as long as you use the proper
>> PSF and parameter files. NAMD doesn't know atom types -- it will
>> match the names in the coordinate file to those in the PSF and the
>> parameter file.
>>
>> Cheers,
>> Rogan
>>
>> On Apr 20, 2009, at 12:42 AM, Gianluca Interlandi wrote:
>>
>>> Is it possible to use NAMD 2.6 (or 2.7b1?) to simulate a system
>>> containing alpha-D-mannose with the new McKerrel's sugar parameter
>>> set top_all35_sugar.inp?
>>> My worry is that NAND will not recognize the longer atom types,
>>> e.g.,
>>> ATOM C1 CC3162
>>> Thanks,
>>>
>>> Gianluca
>>> -----------------------------------------------------
>>> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
>>> +1 (206) 685 4435
>>> +1 (206) 714 4303
>>> http://artemide.bioeng.washington.edu/
>>> Postdoc at the Department of Bioengineering
>>> at the University of Washington, Seattle WA U.S.A.
>>> -----------------------------------------------------
>>
>>
>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
> +1 (206) 685 4435
> +1 (206) 714 4303
> http://artemide.bioeng.washington.edu/
>
> Postdoc at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------

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