# Preparing Haddock dimer for Amber MD simulation

**URL:** https://ask.bioexcel.eu/t/preparing-haddock-dimer-for-amber-md-simulation/5022
**Category:** HADDOCK
**Created:** [May 20, 2024, 2:51pm UTC](https://ask.bioexcel.eu/t/preparing-haddock-dimer-for-amber-md-simulation/5022 "2024-05-20T14:51:23Z")
**Posts on this page:** 3
**Page:** 1

<div class="post-metadata">

### Author: ![marco99](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/marco99/32/975_2.png) [@marco99](https://ask.bioexcel.eu/u/marco99)
#### Post date: [May 20, 2024, 2:51pm UTC](https://ask.bioexcel.eu/t/preparing-haddock-dimer-for-amber-md-simulation/5022/1 "2024-05-20T14:51:23Z")

</div>

Dear prof Bovin et al,

I’m having some problems performing MD simulations with the dimer I obtained from HADDOCK.

I used Haddock to dock two proteins and to obtain a dimer. I tried to prepare the dimer for a MD simulation with Amber, but I’m obtaining 300 errors like the following:

> check dimer  
> Checking ‘dimer’…

> Warning: The unperturbed charge of the unit (-10.000000) is not zero.  
> FATAL: Atom .R\<NALA 1\>.A\< **HN** 13\> does not have a type.  
> FATAL: Atom .R\<THR 2\>.A\<HN 15\> does not have a type.  
> FATAL: Atom .R\<LYS 3\>.A\<HN 23\> does not have a type.  
> FATAL: Atom .R\<ALA 4\>.A\<HN 11\> does not have a type.  
> FATAL: Atom .R\<VAL 5\>.A\<HN 17\> does not have a type.  
> FATAL: Atom .R\<GLY 302\>.A\<HN 8\> does not have a type.  
> FATAL: Atom .R\<VAL 303\>.A\<HN 17\> does not have a type.  
> FATAL: Atom .R\<ILE 304\>.A\<HN 20\> does not have a type.  
> FATAL: Atom .R\<GLY 305\>.A\<HN 8\> does not have a type.  
> FATAL: Atom .R\<ILE 306\>.A\<HN 20\> does not have a type.  
> FATAL: Atom .R\<ALA 307\>.A\<HN 11\> does not have a type.  
> FATAL: Atom .R\<CGLN 308\>.A\<HN 19\> does not have a type.  
> FATAL: Atom .R\< **ZN2** 309\>.A\< **ZN+2** 1\> does not have a type.  
> FATAL: Atom .R\< **CU2** 310\>.A\< **CU+2** 1\> does not have a type.

The PDB file of the dimer is here loaded:  
[wt\_wt\_holo.pdb](https://ask.bioexcel.eu/uploads/short-url/lp4DGtW6d1wkv4m7MDZR8BAMMF5.pdb) (217.6 KB)

Note that the monomer worked fine and it was loaded correctly.

So for the dimer I tried with a python script to change atom types: HN into H, ZN+2 into ZN, , CU+2 into CU and residues type: ZN2 into ZN and CU2 into CU, it seems Amber it doesn’t like them.

The new PDB file with those corrections is:  
[wt\_wt\_holo\_new.pdb](https://ask.bioexcel.eu/uploads/short-url/w12nMH6XDfStttIbzcqjh0XRgGM.pdb) (218.1 KB)

Comparing the two PDB files, it seems that che code was effective.

However I got two more errors now when I try to load the new PDB in Amber:

> check dimer  
> Checking ‘dimer’…

> Warning: The unperturbed charge of the unit (-2.000000) is not zero.  
> FATAL: Atom .R\<NALA 1\>.A\<H 13\> does not have a type.  
> FATAL: Atom .R\<NALA 156\>.A\<H 13\> does not have a type.

It seems that the fact that I renamed HN into H, had no effect on residue 1 and 156.

I forgot to mention that before loading each PDB file in amber, I used the following instruction:

pdb4amber -i \<dimer.pdb\> -o \<dimer\_for\_amber.pdb\>

After those corrections, also the charge changed (from -10 to -2) but I can’t find the reason for that.

Sorry for the long question, I hope I can have some guidelines to make this work, thank you very much in advance.

Have a nice day  
Marco

---

<div class="post-metadata">

### Author: ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [May 20, 2024, 4:12pm UTC](https://ask.bioexcel.eu/t/preparing-haddock-dimer-for-amber-md-simulation/5022/2 "2024-05-20T16:12:42Z")

</div>

Sorry but we can’t help you with this

---

<div class="post-metadata">

### Author: ![marco99](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/marco99/32/975_2.png) [@marco99](https://ask.bioexcel.eu/u/marco99)
#### Post date: [May 20, 2024, 4:27pm UTC](https://ask.bioexcel.eu/t/preparing-haddock-dimer-for-amber-md-simulation/5022/3 "2024-05-20T16:27:12Z")

</div>

Thank you for the response, I think I will ask about this problem in amber forums.  
Have a great day  
Marco