Yep, contrary to AMBER, GMX is not case sensitive, so C and c are the same and since you declare them twice you get this overriding warning.
However, I did acpypi aware of this (it should add '_' to e.g. c, making 'c_'). Unless you're doing something manually (as it seems). Otherwise it would a pleasure to see this issue closely (can you send me your input prmtop and inpcrd?). Otherwise do it yourself by making c_ and o_ and the overriding warn will be off. Cheers, Alan > > Message: 7 > Date: Thu, 4 Jun 2009 20:55:52 +0000 > From: Rebeca Garc?a Fandi?o <rega...@hotmail.com> > Subject: [gmx-users] overrriding problem > To: <gmx-users@gromacs.org> > Message-ID: <bay142-w269f0995d7f3b4890e330db7...@phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > Hi, > I am doing a simulation combining amber and Gaff force field (for dopc > lipids), this is the first part of my topology file: > > ; UNK_GMX.top created by acpypi on Thu Jun 4 22:06:03 2009 > > [ defaults ] > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > 1 2 yes 0.5 0.8333 > > [ atomtypes ] > ;name bond_type mass charge ptype sigma epsilon > Amb > CA CA 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; > 1.91 0.0860 > CT CT 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; > 1.91 0.1094 > C C 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; > 1.91 0.0860 > HO HO 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; > 0.00 0.0000 > O O 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; > 1.66 0.2100 > OH OH 0.00000 0.00000 A 3.06647e-01 8.80314e-01 ; > 1.72 0.2104 > c3 c3 12.0100 -0.12654 A 3.399676e-01 > 4.577296e-01 ; 1.91 0.1094 > hc hc 1.0080 0.02245 A 2.649538e-01 > 6.568880e-02 ; 1.49 0.0157 > c2 c2 12.0100 -0.15458 A 3.399676e-01 > 3.598240e-01 ; 1.91 0.0860 > ha ha 1.0080 0.11146 A 2.599647e-01 > 6.276000e-02 ; 1.46 0.0150 > c c 12.0100 0.44800 A 3.399676e-01 > 3.598240e-01 ; 1.91 0.0860 > o o 16.0000 -0.47180 A 2.959927e-01 > 8.786400e-01 ; 1.66 0.2100 > os os 16.0000 -0.15429 A 3.000018e-01 > 7.112800e-01 ; 1.68 0.1700 > h1 h1 1.0080 0.16551 A 2.471358e-01 > 6.568880e-02 ; 1.39 0.0157 > p5 p5 30.9700 1.14364 A 3.741781e-01 > 8.368000e-01 ; 2.10 0.2000 > n4 n4 14.0100 0.01626 A 3.250004e-01 > 7.112800e-01 ; 1.82 0.1700 > hx hx 1.0080 0.08244 A 1.959981e-01 > 6.568880e-02 ; 1.10 0.0157 > OW OW 0.00000 0.00000 A 3.16572e-01 6.49775e-01 ; > 1.78 0.1553 > HW HW 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; > 0.00 0.0000 > Na Na 0.00000 0.00000 A 2.15954e-01 1.47545e+00 ; > 1.21 0.3526 > Cl Cl 0.00000 0.00000 A 4.83045e-01 5.34924e-02 ; > 2.71 0.0128 > > When I try to minimize the system, with grompp -f minimizado.mdp -c > final_system.gro -p final_system.top -o minimizado.tpr I find 2 warnings: > > WARNING 1 [file final_system.top, line 19]: > Overriding atomtype c > WARNING 2 [file final_system.top, line 20]: > Overriding atomtype o > > It is like it is not distinguing the capitals for amber and non-capitals > for gaff. Does anybody know which can be the cause of these warnings? > > Thank you very much, > > Rebeca Garcia > University of Oxford > -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<<
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