From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Wed Jul 16 2014 - 00:32:49 CDT
I'm cc'ing here the NAMD list so that others can read this, too.
In the CHARMM gui website, there is nothing to download. Just click on
"Input Generator" on the left side. Then, you can for example click on
either "PDB Reader" or "Quick MD Simulator". You can enter there the PDB
ID of your molecule or upload a PDB file. It should generate force field
and input files for you.
I'm not sure whether they have tutorials but they also have some video
demos:
http://www.charmm-gui.org/?doc=demo
Good luck!
Gianluca
On Wed, 16 Jul 2014, Abhishek TYAGI wrote:
> Dear Gianluca,
>
> Thankyou for your reply, I further want to ask that how to get access to
> CHARMM gui, I want to use it and want to learn it for better MDS
> results. I should be highly thankful to you if you suggest me how to
> start for this. It look silly to you but I searched the website but
> unable to find the download and tutorials. I am new to CHARMM but I
> understand it is important to learn.
>
> regards
>
> Abhi
> ________________________________________
> From: Gianluca Interlandi <gianluca_at_u.washington.edu>
> Sent: Wednesday, July 16, 2014 11:32 AM
> To: Abhishek TYAGI
> Cc: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: Force field design
>
> If you are familiar with the CHARMM program, a good resource is:
>
> http://www.charmm-gui.org/
>
> But for that, of course, you would need very good knowledge of the CHARMM
> program (you might even have to even obtain a copy of it which is not
> free).
>
> Gianluca
>
> On Tue, 15 Jul 2014, Abhishek TYAGI wrote:
>
>> I want to run MD, but unfortunately I do not have the reasonable force field for this molecule.
>>
>> Now what I tried following approaches to get force field:
>>
>> 1. I tried CGenFF and got a *.str file but the data in the file is different from my input file i.e. mol2 file, the pdb format is different from the *.str file.
>>
>> 2. I tried to get force field from swissparam website and received the different file as *.par, *.top file, I tried MD on this field it runs successful, but the question is that is this correct approach?
>>
>> 3. I tried parameter tool available in VMD too I got some output from it too, but I am not able to connect all the information.
>>
>> Any guess what to do to get accurate force field parameter for the molecule
>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
> +1 (206) 685 4435
> http://artemide.bioeng.washington.edu/
>
> Research Assistant Professor 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
http://artemide.bioeng.washington.edu/
Research Assistant Professor at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------
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