[gmx-users] Do I need to add hydrogens?

Madhuri Agashe magashe at CLEMSON.EDU
Fri Jan 23 02:54:00 CET 2004

I had further questions:

1. why should we not use ffgmx2 forcefield?

2.how is OPLS better than ffgmx2?

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?

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

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?

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.
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