[gmx-users] The solvation free energy of a vdw ligand

[Tanping Li]

Hey Justin,

Thanks for the help. There is a ligand in my system, whose top file comes from the PRODRG package. PRODRG package only gives the ffgmx force field. Could ffgmx ligand combine protein with other force field? I would be happy to transfer to the newer force field if my system allows. Thanks again and have a good weekend!


Tanping   

--- On Fri, 2/17/12, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> From: Justin A. Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] The solvation free energy of a vdw ligand
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Date: Friday, February 17, 2012, 1:38 PM
> 
> 
> Tanping Li wrote:
> > Hey Justin,
> > 
> > Thanks for the help. I've generated big size of data so
> I hope I can find the way to fix the problem before transfer
> to the new version.
> > 
> > I just find that it gives me problem when I use the
> self-defined atom type in the state B, however works fine if
> I use the existing atom type in the state B.
> > 
> > I defined the atom types by the following way:
> > 
> > [ atometypes ]
> > ;name      mass 
>    charge  Ptype  C6  C12
> > dum_CH3    15.035 
>    0       A 
>    0   0
> > ....
> > ....
> > 
> > 
> > Did I missed some there? I noticed that the "at. num"
> is included in the ffgmxnb.itp file. I searched the manual,
> but haven't find that.
> > 
> 
> It's the atomic number.  Different force fields have
> their lines parsed differently, unfortunately, so you have
> to adhere to the existing format.  Add a zero in the
> column for atom number and see if this improves the
> situation.  I would recommend not using ffgmx for
> anything, though.  The newer manual gives several
> reasons why it's a bad choice for just about any modern
> simulation.
> 
> -Justin
> 
> -- ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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