<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:10pt">On Wed, 26 Jan 2011 at 22:06:47 +0100 (CET), "battistia@libero.it" <battistia@libero.it> wrote:<br><br>I am forwarding this to the Gromacs Users' list because that is the<br>appropriate place for this.<br><br>>excuse me if I am writing you directly. I read on gromacs web page your <br>>advise about the implicit water, and I need to solve a problem for my phD work.<br><br>While at my age I could easily have forgotten writing some off hand comment<br>at some time, I do not recall that I ever gave any advice about implicit water.<br>To the best of my knowledge, I have never used it. The only comment I<br>can recall giving about water concerned not using -DFLEXIBLE in MD runs.<br><br>>Can you help me about my problem? It is possible for you? anywhey very very
<br>>thanks!<br>><br>>My problem:<br><br>Your problem is an example of why all gromacs questions should be sent to<br>the user's list rather than sending them privately. I absolutely do not have<br>any clue why grompp does not pick up the gbsa.itp file you mention below,<br>but I am sure somebody else might.<br><br>>For my system I defined an atomtype in this way:<br>>(I defined about 10 atoms type and for all I have got the same problem)<br>><br>>[ atomtypes ]<br>>; name bond_type mass charge ptype sigma(nm) epsilon(kj/mol)<br>>NLAPT NC 14.0067 0.314 A 0.29760 0.87672<br>><br>><br>>if in the md.mdp file I set<br>>; IMPLICIT SOLVENT
ALGORITHM<br>>implicit_solvent = no<br>><br>>grompp tool give a good result, and mdrun can generate the good trajectories, <br>>but if I use the implicit solvent : implicit_solvent = GBSA<br>><br>>the tool grompp give the error:<br>><br>>GB parameter(s) missing or negative for atom type 'NLAPT'<br>><br>>Fatal error:<br>>Can't do GB electrostatics; the implicit_genborn_params section of the<br>>forcefield is missing parameters for 8 atomtypes or they might be negative.<br>>For more information and tips for troubleshooting, please check the GROMACS<br><span>>website at <a target="_blank" href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a></span><br>><br>><br>>so I put the following parameter in the gbsa.itp file the parameter:<br>><br>>[
implicit_genborn_params ]<br>><br>>; atype sar st pi gbr hct<br>>NLAPT 0.155 1 1.028 0.1488 0.79 ; N<br>><br>><br>>but grompp give the error<br>><br>>Couldn't find topology match for atomtype NLAPT<br>>Aborted<br>><br>><br>>Can you give me an idea in order to solve this problem?<br>>Thank you very much!!!<br><div><br>My idea is that you should keep all gromacs related correspondence on<br>the gromacs users' e-mail list where somebody who actually knows<br>something might see it.<br><br><br>Sincerely,<br><br><br></div>-- <br>Bruce D. Ray, Ph.D.<br>Associate Scientist<br>IUPUI<br>Physics Dept.<br>402 N. Blackford
St.<br>Indianapolis, IN 46202-3273<div><br></div>
</div><br>
</body></html>