[gmx-users] Re: Atom O5 not found in residue seq.nr. 1 while adding atom

[pragna lakshmi]

I forgot to mention that i am using OPLS-AA/L all-atom force field.

On Fri, Mar 9, 2012 at 11:21 AM, pragna lakshmi <pragnapcu at gmail.com> wrote:

> Dear Gromacs Users,
>                 I need to simulate a protein that has N-acetyl glucosamine
> (NAG). Since NAG residue is not present in residue topology file, first of
> all i added NAG parameters to aminoacids.rtp file. I am following this link
> *
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
> *
>
> This is my aminoacids.rtp file for NAG.
>
> [ NAG ] ; N-Acetylglucosamine
>
> [ atoms ]
>    C1    opls_195   +0.365    1
>   HC1    opls_196   +0.100    1
>    O1    opls_187   -0.700    1
>   HO1    opls_188   +0.435    1
>    C5    opls_183   +0.170    1
>   HC5    opls_185   +0.030    1
>    O5    opls_180   -0.400    1
>    C2    opls_229   +0.140    2
>   HC2    opls_140   +0.060    2
>    N2    opls_238   -0.500    2
>   N15    opls_238   -0.500    2
>   HN2    opls_241   +0.300    2
>    C3    opls_158   +0.205    3
>   HC3    opls_140   +0.060    3
>    O3    opls_154   -0.683    3
>   O3H    opls_155   +0.418    3
>   O2H    opls_155   +0.418    3
>    C4    opls_158   +0.205    4
>   HC4    opls_140   +0.060    4
>    O4    opls_154   -0.683    4
>    OM    opls_154   -0.683    4
>   O4H    opls_155   +0.418    4
>    C6    opls_157   +0.145    5
> HC61    opls_140   +0.060    5
> HC62    opls_140   +0.060    5
>    O6    opls_154   -0.683    5
>   O6H    opls_155   +0.418    5
>    C7    opls_235   +0.500    6
>    O7    opls_236   -0.500    6
>    C8    opls_135   -0.180    7
> HC81    opls_140   +0.060    7
> HC82    opls_140   +0.060    7
> HC83    opls_140   +0.060    7
>   OR    opls_154   -0.683    5
>   OW    opls_154   -0.683    5
>
> [ bonds ]
>    C1  HC1
>    C1   O1
>    C1   C2
>    C1   O5
>    O1  HO1
>    C2  HC2
>    C2   N2
>    C2   C3
>    N2  HN2
>    N2   C7
>    C3  HC3
>    C3   O3
>    C3   C4
>    O3  HO3
>    C4  HC4
>    C4   O4
>    C4   C5
>    O4  HO4
>    C5  HC5
>    C5   O5
>    C5   C6
>    C6 HC61
>    C6 HC62
>    C6   O6
>    O6  HO6
>    C7   O7
>    C7   C8
>    C8 HC81
>    C8 HC82
>    C8 HC83
>
> Now i have got this error.
>
> Fatal error:
> Atom O5 not found in residue seq.nr. 1 while adding atom
>
> If any body knows solution for this, can you please reply this. If any
> error is there in aminoacids.rtp file, please mention it. I will change it
> accordingly. Any suggestion is appreciable.
>



-- 
T.Pragna Lakshmi,
Junior Scientist,
Vision Research Center,
Sankara Netralaya,
Chennai,
India.
Pin: 600006.
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