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 <[email protected]>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 <[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. 1 while adding atom >> > > Your coordinate file doesn't match your .rtp entry regarding atom O5. > > Mark > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- T.Pragna Lakshmi, Junior Scientist, Vision Research Center, Sankara Netralaya, Chennai, India. Pin: 600006.
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