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

[pragna lakshmi]

Thank u so much Mark. Is there any parameterization to mention forcefield
and co ordinates in aminoacids.rtp in the fields of atoms, bonds (like
C1    opls_195   +0.365    1 ). I checked the co ordinates in .pdb and .rtp
files. Both are not the same.



On Fri, Mar 9, 2012 at 11:56 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  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>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
>>
>
> Your coordinate file doesn't match your .rtp entry regarding atom O5.
>
> Mark
>
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-- 
T.Pragna Lakshmi,
Junior Scientist,
Vision Research Center,
Sankara Netralaya,
Chennai,
India.
Pin: 600006.
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