Re: NAMD and new sugar parameter set

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Mon Apr 20 2009 - 15:39:31 CDT

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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