[gmx-users] Do I need to add hydrogens?
spoel at xray.bmc.uu.se
Fri Jan 23 07:47:01 CET 2004
On Fri, 2004-01-23 at 02:53, Madhuri Agashe wrote:
> I had further questions:
> 1. why should we not use ffgmx2 forcefield?
it is exactly the same as ffgmx, with hydrogens as place holders for NMR
> 2.how is OPLS better than ffgmx2?
THis is under debate, but for organic liquids it is probably more well
tuned than gromos
> 3.How should one go about using OPLS given the fact that gromacs first looks
> for the .rtp and .atp files in usr/local/share/gromacs/top?
opls files are also there. just include "ffoplsaa.itp" and use the
appropriate opls atom types
> 4.In octanol.itp that you had attached to the previous reply, Carbons are
> defined with no hydrogens wheras oxygen has a hydrogen defined too. Why is
> this so? Does this mean that hydrogens attached to carbons need not be
correct, united atoms, see manual
> 5. The gromacs library has decane.itp. This molecule has ONLY carbons
> defined and no hydrogens. Does this mean that while defining alkane/alkene
> chains, we do not need to define hydrogens?
> 6. When a Carbon is defined as a C2 carbon, does it assume 2 implicit
> hydrogens? Is this Carbon so parameterized so as to include the effect of
> these implicit hydrogens?
In ffgmx2 and opls you will have to add hydrogens using the .hdb file
mechanism (chapter 5 in th e manual)
> We look forward to these answers. They are very crucial for our research!!
> -----Original Message-----
> From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org] On
> Behalf Of David
> Sent: Thursday, January 22, 2004 12:31 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Do I need to add hydrogens?
> On Wed, 2004-01-21 at 22:02, Vivek Raut wrote:
> > Hi,
> > I am trying to introduce a new molecule in gromacs residue topology
> > database. The molecular structure is:
> > CH3-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-OH
> > In order to get this molecule recognized by gromacs, I have added the
> > following part in ffgmx2.rtp file.
> Please do not use this force field anymore. Check the attached united
> atom topology for octanol, or make one using OPLS force field. Do also
> check a recent McCallum & Tieleman paper on octanol where they have
> updated the force field parameters.
> > To make this addition I took the decane molecule, which is already present
> > in gromacs residue file, as a guideline.
> > I have 2 questions on this:
> > 1: it is ok NOT to include hydrogens in the .rtp file as well as .pdb file
> > while making a molecule? ( as there were no hydrogens included in Decane &
> > I suppose gromacs automatically adds the hydrogens to complete the
> > molecules). Is it ALLOWED in gromacs?
> No gromacs does not do it automatically, you will have to specify what
> you want in the corresponding .hdb file.
> > 2: Am I doing something wrong in introducing a new molecule to gromacs by
> > adding something in .rtp file?
> > 3: If I have to add hydrogens, wont the .rtp file be too complicated after
> > including all the hydrogen bonds, angles & dihedrals?. What can be done in
> > this case?
> If you'd want OPLS you could do it this way.
> > -
> > thank you.
> > --
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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