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

[David]

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.
________________________________________________________________________
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-------------- next part --------------
[ moleculetype ]
; Name	nrexcl
Octanol	3

[ atoms ] 
; nr    type   	resnr  	residu  atom  	cgnr	charge
1	CH3	1	OCT	C1	1	0.0
2	CH2	1	OCT	C2	2	0.0
3	CH2	1	OCT	C3	3	0.0
4	CH2	1	OCT	C4	4	0.0
5	CH2	1	OCT	C5	5	0.0
6	CH2	1	OCT	C6	6	0.0
7	CH2	1	OCT	C7	7	0.0
8	CH2	1	OCT	C8	8	0.15
9	OA	1	OCT	O9	8	-0.548
10	HO	1	OCT	H10	8	0.398

[ bonds ]
; i	j
1	2
2	3
3	4
4	5
5	6
6	7
7	8
8	9
9	10

[ angles ]
; i	j	k
1	2	3
2	3	4
3	4	5
4	5	6
5	6	7
6	7	8
7	8	9
8	9	10

[ dihedrals ]
; i	j	k 	l	type
1 	2	3	4	3
2	3	4	5	3
3	4	5	6	3
4	5	6	7	3
5	6	7	8	3
6	7	8	9	1
7	8	9	10	1

#ifdef POSRES
[ position_restraints ]
; i	func	fx	fy	fz
5	1	1000	1000	1000
8	1	1000	1000	1000
#endif

#ifdef WEAKPOSRES
[ position_restraints ]
; i	func	fx	fy	fz
5	1	100	100	100
8	1	100	100	100
#endif