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I want to md simulation ssdna.I have modelled ssdna and have ssdna.pdb files.before run md simulation,I renamed all the atoms using charmm27.ff/dna.rtp.
When I given the command …pdb2gmx -f … -o … -p … -ignh
I gate the following error Fatal error: Residue ‘T’ not found in residue topology database
please how to fix these error ?
This comes up all the time:
Check the available residue names, and update your coordinate file to use proper residue names that match the force field’s expectations.
ATOM 129 P T A 5 -14.272 -5.226 13.461 1.00 0.00 P
ATOM 130 CN8B T A 5 -16.064 -3.510 12.590 1.00 0.00 C
ATOM 131 ON2 T A 5 -15.223 -4.633 12.329 1.00 0.00 O
ATOM 132 CN7 T A 5 -16.962 -3.243 11.404 1.00 0.00 C
ATOM 133 ON6 T A 5 -16.159 -2.807 10.275 1.00 0.00 O
ATOM 134 CN7 T A 5 -17.711 -4.450 10.863 1.00 0.00 C
ATOM 135 ON2 T A 5 -18.878 -4.733 11.630 1.00 0.00 O
ATOM 136 CN8 T A 5 -18.033 -4.017 9.438 1.00 0.00 C
ATOM 137 CN7B T A 5 -16.766 -3.241 9.069 1.00 0.00 C
ATOM 138 NN2B T A 5 -15.781 -4.044 8.303 1.00 0.00 N
ATOM 139 CN1T T A 5 -16.062 -4.286 6.987 1.00 0.00 C
ATOM 140 ON1 T A 5 -17.063 -3.872 6.434 1.00 0.00 O
ATOM 141 NN2U T A 5 -15.116 -5.038 6.309 1.00 0.00 N
ATOM 142 CN1 T A 5 -13.949 -5.553 6.830 1.00 0.00 C
ATOM 143 ON1 T A 5 -13.180 -6.214 6.123 1.00 0.00 O
ATOM 144 CN3T T A 5 -13.753 -5.247 8.229 1.00 0.00 C
ATOM 145 CN3 T A 5 -14.647 -4.521 8.911 1.00 0.00 C
ATOM 146 C5M T A 5 -12.494 -5.791 8.839 1.00 0.00 C
ATOM 147 ON3 T A 5 -15.059 -5.347 14.715 1.00 0.00 O
ATOM 148 ON3 T A 5 -13.583 -6.420 12.910 1.00 0.00 O
ATOM 149 HN8 T A 5 -16.684 -3.709 13.463 1.00 0.00 H
ATOM 150 HN2 T A 5 -15.304 -5.231 5.314 1.00 0.00 H
ATOM 151 HN3 T A 5 -14.471 -4.305 9.964 1.00 0.00 H
ATOM 152 HN7 T A 5 -16.990 -2.346 8.487 1.00 0.00 H
ATOM 153 HN5 T A 5 -18.174 -4.886 8.794 1.00 0.00 H
ATOM 154 HN7 T A 5 -17.099 -5.350 10.898 1.00 0.00 H
ATOM 155 HN7 T A 5 -17.713 -2.515 11.713 1.00 0.00 H
ATOM 156 HN8 T A 5 -15.453 -2.628 12.783 1.00 0.00 H
ATOM 157 HN9 T A 5 -12.124 -6.618 8.233 1.00 0.00 H
ATOM 158 HN9 T A 5 -11.740 -5.006 8.879 1.00 0.00 H
ATOM 159 HN9 T A 5 -12.703 -6.146 9.849 1.00 0.00 H
ATOM 160 HN8 T A 5 -18.909 -3.368 9.416 1.00 0.00 H
I renamed all the atoms again from charmm27.rtp and top_all27_na.rtf and ı still getting same error
what else should i do ?
Start over. You’ve replaced the atom names with atom types, which will fail. The problem is the residue name. T is not a valid residue, but DT is. Note you won’t find any entry “T” in either the original CHARMM files (which is THY) or in GROMACS (DT).
dear doctor,I am so beginner.
What do I have to do as a starting step ?
What do I have to change first ?
please could you help me ?
My last post contained the solution. Refer also to the link I provided, which explains the background of the error in more detail.
hello sir
iI am doing md simulation for pha polymer in chloroform and have the same error, I try to add the .rtp file manually to the opls-aa force field but did not work can you give other advice please