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 <[email protected]
<mailto:[email protected]>> 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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