# Residue 'T' not found in residue topology database
**URL:** https://gromacs.bioexcel.eu/t/residue-t-not-found-in-residue-topology-database/1186
**Category:** User discussions
**Created:** [December 2, 2020, 7:11pm UTC](https://gromacs.bioexcel.eu/t/residue-t-not-found-in-residue-topology-database/1186 "2020-12-02T19:11:02Z")
**Posts on this page:** 7
**Page:** 1
### Author:  [@imrbay](https://gromacs.bioexcel.eu/u/imrbay)
#### Post date: [December 2, 2020, 7:11pm UTC](https://gromacs.bioexcel.eu/t/residue-t-not-found-in-residue-topology-database/1186/1 "2020-12-02T19:11:02Z")
GROMACS version:
GROMACS modification: Yes/No
Here post your question
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 ?
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### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [December 2, 2020, 7:45pm UTC](https://gromacs.bioexcel.eu/t/residue-t-not-found-in-residue-topology-database/1186/2 "2020-12-02T19:45:18Z")
This comes up all the time:
> **[Common errors when using GROMACS — GROMACS 2020.4 documentation](http://manual.gromacs.org/current/user-guide/run-time-errors.html#residue-xxx-not-found-in-residue-topology-database)**
Check the available residue names, and update your coordinate file to use proper residue names that match the force field’s expectations.
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### Author:  [@imrbay](https://gromacs.bioexcel.eu/u/imrbay)
#### Post date: [December 2, 2020, 9:12pm UTC](https://gromacs.bioexcel.eu/t/residue-t-not-found-in-residue-topology-database/1186/3 "2020-12-02T21:12:57Z")
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 ?
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### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [December 2, 2020, 9:29pm UTC](https://gromacs.bioexcel.eu/t/residue-t-not-found-in-residue-topology-database/1186/4 "2020-12-02T21:29:16Z")
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).
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### Author:  [@imrbay](https://gromacs.bioexcel.eu/u/imrbay)
#### Post date: [December 3, 2020, 9:27am UTC](https://gromacs.bioexcel.eu/t/residue-t-not-found-in-residue-topology-database/1186/5 "2020-12-03T09:27:41Z")
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 ?
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### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [December 4, 2020, 1:52am UTC](https://gromacs.bioexcel.eu/t/residue-t-not-found-in-residue-topology-database/1186/6 "2020-12-04T01:52:30Z")
My last post contained the solution. Refer also to the link I provided, which explains the background of the error in more detail.
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### Author:  [@faresdiaeddine](https://gromacs.bioexcel.eu/u/faresdiaeddine)
#### Post date: [December 4, 2023, 12:07pm UTC](https://gromacs.bioexcel.eu/t/residue-t-not-found-in-residue-topology-database/1186/7 "2023-12-04T12:07:43Z")
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