From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Mon Jul 21 2014 - 10:47:12 CDT
This list is full of very knowledgeable people who are very good at
resolving people's errors, but even the greatest guru cannot help you if
you don't tell them what exactly your problem is.
Since I get the impression you're relatively new to this, allow me to link
you to CHARMM's "parameter set discussion" forum guide lines:
I'm NOT suggesting you ask your question there. The CHARMM forums are for
CHARMM problems and the regulars don't like it if you post VMD/NAMD
problems. For NAMD, this mailinglist it the correct support channel.
Rather, the reason I'm giving you this link is that most of the good
practices it outlines are valid in *any* technical community, including
this list. In a nutshell, you are advised to search the web, consult the
valid resources (tutorials, FAQs...), experiment a bit yourself and
consult your advisor/mentor/senior postdoc before asking a question. Then,
if you must ask a question, take plenty of time formulating it, thinking
of it from the point of view of the expert trying to answer it. Make it
concise but include all relevant information.
On 07/19/2014 08:44 AM, Abhishek TYAGI wrote:
> Dear Kenno,
> Thankyou for the suggestion, I had read all the information provided so far and gone through the links in detail. But still I have a silly question, right now I have a.mol2 file and I got CGenFF a.str file, and for psfgen If I use a.str file it shows error, therefore I used CHARM-GUI to get psf and pdb file, I tried doe quick md on C-GUI it gives some topology and prm file, I used them for my simulation and got error, and for other files top and prm I still confused how to proceed.
> From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Kenno Vanommeslaeghe <kvanomme_at_rx.umaryland.edu>
> Sent: Thursday, July 17, 2014 1:24 AM
> To: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: Force field design
> On 07/15/2014 12:55 PM, Abhishek TYAGI wrote:
>> 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.
> The str file contains a force field for your molecule, while the mol2 and
> pdb formats contain a geometry. How could the data not be different???
> The str file is a concatenated topology and parameter file. NAMD knows to
> ignore the topology section and can read the file as it is.
> I believe psfgen does the same (read the topology and ignore the
> parameters) though I'm less sure about that.
>> 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?
> It is strongly encouraged to search the archive before posting a question.
> If you had, you would have discovered the use of SwissParam for
> condensed-phase calculations is discouraged, and found advise on better
> ways to do it:
> Christopher Mayne's advice in this thread is sound.
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