[gmx-users] overrriding problem

[Rebeca García Fandiño]

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

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