[gmx-users] which force field to select!

[Itamar Kass]

  Good questions, I will try working without the hydrogen atoms (united atoms
force field) try the standard one – Gromos87. But, you can add the hydrogen by
hand.

Cheers, Itamar.


Quoting Prettina Anto_Louis <pretti_louis at krify.com>:

> Hello gromacs users,
>    Greetings!
>          I am working with a docked complex. At present I am using GROMACS
> Dynamics simulation for my work. As a part of that I am using PRODRG server
> also for the inhibitor for which i need the gro coordinates and topology
> file. But when i submit the pdb coordinates of the same with hydrogens, it
> deletes the hydrogen from the inhibitor and gives the output. But I need the
> hydrogens to run the simulation.
>
> The following is the output which i got:
>
> ========
> PRODRG> Starting up PRODRG version 050728.0532
> PRODRG> PRODRG written/copyrighted by Daan van Aalten
> PRODRG>
> PRODRG> Questions/comments to dava at davapc1.bioch.dundee.ac.uk
> PRODRG>
> PRODRG> When using this software in a publication, cite:
> PRODRG> A. W. Schuettelkopf and D. M. F. van Aalten (2004).
> PRODRG> PRODRG - a tool for high-throughput crystallography
> PRODRG> of protein-ligand complexes.
> PRODRG> Acta Crystallogr. D60, 1355--1363.
> PRODRG>
> PRODRG>
> PRODRG> PDB mode detected.
> PRODRG> WARNING: deleted hydrogen 1H1  from your input.
> PRODRG> WARNING: deleted hydrogen 2H1  from your input.
> PRODRG> WARNING: deleted hydrogen 1H2  from your input.
> PRODRG> WARNING: deleted hydrogen 2H2  from your input.
> PRODRG> WARNING: deleted hydrogen 1H6  from your input.
> PRODRG> WARNING: deleted hydrogen 2H6  from your input.
> PRODRG> WARNING: deleted hydrogen 1H7  from your input.
> PRODRG> WARNING: deleted hydrogen 2H7  from your input.
> PRODRG> WARNING: deleted hydrogen 3H7  from your input.
> PRODRG> WARNING: deleted hydrogen 1H8  from your input.
> PRODRG> WARNING: deleted hydrogen 2H8  from your input.
> PRODRG> WARNING: deleted hydrogen 3H8  from your input.
> PRODRG> WARNING: deleted hydrogen 1H9  from your input.
> PRODRG> WARNING: deleted hydrogen 2H9  from your input.
> PRODRG> WARNING: deleted hydrogen 1H10 from your input.
> PRODRG> WARNING: deleted hydrogen 2H10 from your input.
> PRODRG> WARNING: deleted hydrogen 1H12 from your input.
> PRODRG> WARNING: deleted hydrogen 2H12 from your input.
> PRODRG> WARNING: deleted hydrogen  H13 from your input.
> PRODRG> WARNING: deleted hydrogen 1H14 from your input.
> PRODRG> WARNING: deleted hydrogen 2H14 from your input.
> PRODRG> WARNING: deleted hydrogen 3H14 from your input.
> PRODRG> WARNING: deleted hydrogen 1H18 from your input.
> PRODRG> WARNING: deleted hydrogen 2H18 from your input.
> PRODRG> WARNING: deleted hydrogen 3H18 from your input.
> PRODRG> Molecule complexity index: 2.00.
> PRODRG> WARNING: applied  1 unusual hybridisation fixup(s).
> PRODRG>  0 hydrogen(s) added.
> PRODRG>  19 bonds                7 ambiguous
> PRODRG>  26 bond angles        11 ambiguous
> PRODRG>  5 improper dihedrals  0 ambiguous
> PRODRG>  13 dihedrals            5 ambiguous
> PRODRG>  3 partial charges      0 ambiguous
> PRODRG> Net charge on molecule:  0.000
> PRODRG> Using charge groups.
> PRODRG> Writing GROMACS topology.
> PRODRG> GROMACS topology quality on 0-10 scale:  6.4
> PRODRG> Keeping old coordinates.
> PRODRG> RMSD from GROMOS bond ideality (Angstrom) :  0.042
> PRODRG> RMSD from GROMOS angle ideality (degrees) :  4.151
> PRODRG> RMSD from GROMOS plane ideality (degrees) :  1.060
> PRODRG> Number of improper improper dihedrals    :      0
> PRODRG> Writing: SCRHWMMPG
> PRODRG> Normal program end
> ==================
>
> please let me know, is there any option to add hydrogens in the gro and top
> file? Please let me know how to proceed with that.Without the hydrogens how
> will i study the interaction between enzyme and drug? If i run the energy
> minimisation without the hydrogens in the inhibitor is it correct? Which
> force field should i select?  How to edit the files for my inhibitor to make
> the simulation work with the enzyme.Please help me out.
>
>     Looking forward to hear from u soon!
>
>     Thanking you!
>
>
>
> "praise the lord!"
>
>
> With prayers,
> prettina
>  
> I use Krify Mail - http://mail.krify.com  Get  yourmail at  Krify today!
>
>




===========================================
| Itamar Kass
| The Alexander Silberman
| Institute of Life Sciences
| Department of Biological Chemistry
| The Hebrew University, Givat-Ram
| Jerusalem, 91904, Israel
| Tel: +972-(0)2-6585194
| Fax: +972-(0)2-6584329
| Email: ikass at cc.huji.ac.il
| Net: http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html
============================================

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