Re: Parameter and Topology File Question

From: Brian Radak (brian.radak_at_gmail.com)
Date: Sun Apr 21 2019 - 12:30:49 CDT

To be clear - unless stated in the materials, all rtf/prm files distributed
with the tutorials are included so that the examples are as repeatable as
possible and are for demonstration purposes only. They are not guaranteed
to be current or even free from error. For actual research projects it
would be wise to obtain alternative files, for example from the MacKerell
group.

Cheers,
BKR

On Sun, Apr 21, 2019, 8:37 AM Victor Kwan <vkwan8_at_uwo.ca> wrote:

> Hello,
>
> Please refer to
> http://mackerell.umaryland.edu/~kenno/cgenff/program.php#namd
>
> Victor
>
> On Sun, Apr 21, 2019 at 5:45 AM Oscar Bastidas <obastida_at_umn.edu> wrote:
>
>> Hello,
>>
>> I have noticed that the introductory tutorial parameter and topology
>> files for starting a NAMD simulation (the protein in the tutorial is
>> ubiquitin) are named:
>>
>> par_all27_prot_lipid.inp
>> top_all27_prot_lipid.inp
>>
>> whereas the names obtained from CHARMM-GUI/CHARMM are:
>>
>> par_all36m_prot.prm
>> top_all36_prot.rtf
>>
>> The files from the tutorial obviously run when following the tutorial for
>> setting up and running a simulation on my home computer, but the files from
>> CHARMM/CHARMM-GUI do not run. Additionally, as I understand it, the
>> tutorial files are somewhat out of date (RMSF profiles from both file
>> sources are vastly different).
>>
>> My question then is, how do I obtain parameter and topology files that
>> are the most recent *that I can use directly into NAMD and VMD* so that
>> both NAMD and VMD will take them like the tutorial files? Preferably, I
>> would like to have NAMD-compatible top and par files that are the
>> equivalent of charmm36m. Thanks.
>>
>> Oscar
>>
>> Oscar Bastidas, Ph.D.
>> Postdoctoral Research Associate
>> University of Minnesota
>>
>

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