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 <pragna...@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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