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.
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