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

[Mark Abraham]

On 9/03/2012 4:56 PM, pragna lakshmi wrote:
> 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 
> <mailto: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 <http://seq.nr>. 1 while
>     adding atom
>

Your coordinate file doesn't match your .rtp entry regarding atom O5.

Mark
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