Date: Fri Sep 09 2016 - 02:51:25 CDT
Thank you for these answers,
for the topology inforation, partials charges and so on I saw the software
vega-zz is maybe a solution so I will try with it and GAAMP.
Again thank you very much!
> This is a common enough problem that several groups are looking into
> (relatively) general solutions for it. Just to advertise the work of my
> colleagues, General Automated Atomic Model Parameterization (GAAMP), is
> one such method. To my knowledge this can be used compatibly with AMBER
> (GAFF) and CHARMM (CGenFF) force fields.
> You can find the GAAMP server here: http://gaamp.lcrc.anl.gov/
> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
> 9700 South Cass Avenue, Bldg. 240
> Argonne, IL 60439-4854
> (630) 252-8643
> From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of
> Axel Kohlmeyer [akohlmey_at_gmail.com]
> Sent: Thursday, September 08, 2016 10:41 AM
> To: NAMD list; grenier_at_cinam.univ-mrs.fr
> Subject: Re: namd-l: convert .xyz file in .psf file for non-protein
> On Thu, Sep 8, 2016 at 11:20 AM, <grenier_at_cinam.univ-mrs.fr> wrote:
>> Dear NAMD users,
>> I am a new user of NAMD MD simulations. I work with this non-protein
>> molecule in attachment. Its structure is alrealy optimized (in DFT), so
>> just want to convert this .XYZfile in .PSFfile to perform MD simulation
>> I search in the mailing list and in different tutorials how to do this
>> I don't find the solution.
> that is because you have a lot of work ahead of you. having an
> optimized geometry is about the least important piece of information
> required for a simulation. a PSF file doesn't contain anything of it.
> what you need instead are assignment of force field atom types,
> (partial) charges, topology information like bonds, angles, dihedrals,
> perhaps impropers. ...and since you are using a non-standard
> molecule/residue, you may have to spend some time deriving and
> determining force field parameters for it. for somebody that is new to
> MD, that is a huge amount of work, and particularly assigning/deriving
> force field parameters can be complex and may require a lot of testing
> and additional computations.
>> So I very appreciate any help to do this
> your best chance to get something going, is probably to find a
> collaborator that has the experience and knowledge in working with
> custom molecules.
>> Benjamin Grenier
>> Cinam CNRS, France
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
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