[gmx-users]Fwd: GROMACS and GBSA implicit water

[Bruce D. Ray]

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 
>thanks!
>
>My problem:

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'
>
>Fatal error:
>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
>Aborted
>
>
>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.


Sincerely,


-- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273



      
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