<ol>
<li>The residue numbering in a PDB file mainly depend on the person who deposited it. There are usually reasons for how things are numbered, but ultimately you should look at PDB file, and check the details on how the structure was obtained. To give you an example, during my PhD I worked on a protein that had some missing residues at the N-terminus. That was because the N-term was very unstable and they didn't manage to crystallise it properly.</li>
<li>You need to check the PDB, but it is possible that the 3 chains have the same residue numbering (A1-200, B1-200). This is common in structures where you have multiple identical sub-units (e.g. dimers).</li>
<li>The lines are merely an artefact. Those lines are the attempt of the engine to draw a single line for all the chains. You go from residue 1850 of chain 1 to residue 1650 of chain 2, and so on. Some tools handle this behaviour, others don't. I would suggest you to parse the PDB yourself and plot (e.g. <code>ggplot</code>) each chain as a layer of the same figures .</li>
<li>It is indeed, but only you can tell if this is good or bad. It really depends on how you calculate the RMSF. Was it on the backbone or on the side-chains? How is your dynamics? High temperature? Does you protein partially unfold? are the chains separating?</li>
</ol>

CC BY-SA 4.0
2021-09-29T04:42:26.870Z
Thanks for your response and clarification to understand the result.
miRastic
CC BY-SA 4.0
2021-08-25T12:38:01.347Z
2021-08-25T12:38:01.347Z
fra
<p>This is RMSF for protein from GROMACS after 100ns simulation-</p>
<p><a href="https://i.sstatic.net/H0QPP.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/H0QPP.png" alt="RMSF Result" /></a></p>
<p>I have few questions-</p>
<ol>
<li>Residue numbers are starting from 1650 to 1850, has it ignore LIG
and HOH as residues?</li>
<li>There are three lines, so are there three chains and their residue number is same?</li>
<li>Are the straight lines connecting these chains or this is kind of loop something?</li>
<li>Since I am seeing 2nm or 20A fluctuation, is the protein quite disturbed?</li>
</ol>

<protein-structure><gromacs><molecular-dynamics>
GROMACS RMSF Result Analysis Problem
# GROMACS RMSF Result Analysis Problem

(Asked by: username_0 on 2021-08-25)

This is RMSF for protein from GROMACS after 100ns simulation-

[![RMSF Result](https://i.sstatic.net/H0QPP.png)](https://i.sstatic.net/H0QPP.png)

I have few questions-

1. Residue numbers are starting from 1650 to 1850, has it ignore LIG
   and HOH as residues?
2. There are three lines, so are there three chains and their residue number is same?
3. Are the straight lines connecting these chains or this is kind of loop something?
4. Since I am seeing 2nm or 20A fluctuation, is the protein quite disturbed?

**Tags:** protein-structure, gromacs, molecular-dynamics

---

## 1 answers

### Answer by username_1 on 2021-08-25. Score: 2 | Accepted answer

1. The residue numbering in a PDB file mainly depend on the person who deposited it. There are usually reasons for how things are numbered, but ultimately you should look at PDB file, and check the details on how the structure was obtained. To give you an example, during my PhD I worked on a protein that had some missing residues at the N-terminus. That was because the N-term was very unstable and they didn't manage to crystallise it properly.
2. You need to check the PDB, but it is possible that the 3 chains have the same residue numbering (A1-200, B1-200). This is common in structures where you have multiple identical sub-units (e.g. dimers).
3. The lines are merely an artefact. Those lines are the attempt of the engine to draw a single line for all the chains. You go from residue 1850 of chain 1 to residue 1650 of chain 2, and so on. Some tools handle this behaviour, others don't. I would suggest you to parse the PDB yourself and plot (e.g. `ggplot`) each chain as a layer of the same figures .
4. It is indeed, but only you can tell if this is good or bad. It really depends on how you calculate the RMSF. Was it on the backbone or on the side-chains? How is your dynamics? High temperature? Does you protein partially unfold? are the chains separating?

> **Comments:**
> **username_0**: Thanks for your response and clarification to understand the result.  

---

