On Wed, 26 Jan 2011 at 22:06:47 +0100 (CET), "battis...@libero.it" <battis...@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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