[gmx-users] Re: goverrriding problem

[Alan]

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 <regafan at hotmail.com>
> Subject: [gmx-users] overrriding problem
> To: <gmx-users at gromacs.org>
> Message-ID: <BAY142-W269F0995D7F3B4890E330DB74B0 at 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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