[gmx-users]Fwd: GROMACS and GBSA implicit water
Bruce D. Ray
brucedray at yahoo.com
Wed Jan 26 22:52:24 CET 2011
On Wed, 26 Jan 2011 at 22:06:47 +0100 (CET), "battistia at libero.it"
<battistia at libero.it> wrote:
I am forwarding this to the Gromacs Users' list because that is the
appropriate place for this.
>excuse me if I am writing you directly. I read on gromacs web page your
>advise about the implicit water, and I need to solve a problem for my phD work.
While at my age I could easily have forgotten writing some off hand comment
at some time, I do not recall that I ever gave any advice about implicit water.
To the best of my knowledge, I have never used it. The only comment I
can recall giving about water concerned not using -DFLEXIBLE in MD runs.
>Can you help me about my problem? It is possible for you? anywhey very very
Your problem is an example of why all gromacs questions should be sent to
the user's list rather than sending them privately. I absolutely do not have
any clue why grompp does not pick up the gbsa.itp file you mention below,
but I am sure somebody else might.
>For my system I defined an atomtype in this way:
>(I defined about 10 atoms type and for all I have got the same problem)
>[ atomtypes ]
>; name bond_type mass charge ptype sigma(nm) epsilon(kj/mol)
>NLAPT NC 14.0067 0.314 A 0.29760 0.87672
>if in the md.mdp file I set
>; IMPLICIT SOLVENT ALGORITHM
>implicit_solvent = no
>grompp tool give a good result, and mdrun can generate the good trajectories,
>but if I use the implicit solvent : implicit_solvent = GBSA
>the tool grompp give the error:
>GB parameter(s) missing or negative for atom type 'NLAPT'
>Can't do GB electrostatics; the implicit_genborn_params section of the
>forcefield is missing parameters for 8 atomtypes or they might be negative.
>For more information and tips for troubleshooting, please check the GROMACS
>website at http://www.gromacs.org/Documentation/Errors
>so I put the following parameter in the gbsa.itp file the parameter:
>[ implicit_genborn_params ]
>; atype sar st pi gbr hct
>NLAPT 0.155 1 1.028 0.1488 0.79 ; N
>but grompp give the error
>Couldn't find topology match for atomtype NLAPT
>Can you give me an idea in order to solve this problem?
>Thank you very much!!!
My idea is that you should keep all gromacs related correspondence on
the gromacs users' e-mail list where somebody who actually knows
something might see it.
Bruce D. Ray, Ph.D.
402 N. Blackford St.
Indianapolis, IN 46202-3273
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