# Problem in generating topology file of a polymer

**URL:** <https://gromacs.bioexcel.eu/t/problem-in-generating-topology-file-of-a-polymer/4757>\
**Category:** User discussions\
**Tags:** pdb2gmx, mdrun, simulation-setup\
**Created:** [September 8, 2022, 12:37pm UTC](https://gromacs.bioexcel.eu/t/problem-in-generating-topology-file-of-a-polymer/4757 "2022-09-08T12:37:35Z")\
**Posts on this page:** 10\
**Page:** 1

<div class="post-metadata">

**Author:** ![saiqa](https://avatars.discourse-cdn.com/v4/letter/s/b19c9b/32.png) [@saiqa](https://gromacs.bioexcel.eu/u/saiqa)\
**Post date:** [September 8, 2022, 12:37pm UTC](https://gromacs.bioexcel.eu/t/problem-in-generating-topology-file-of-a-polymer/4757/1 "2022-09-08T12:37:35Z")

</div>

GROMACS version:gmx, version 2022.2  
GROMACS modification: Yes/No  
Here post your question  
The problem I am facing is regarding the topology file generation of my system. A polymer (PEO (polyethylene oxide) e.g. 1 peo= 5EO monomer) is the long chain of a single monomer. I tried to generate a gromacs readable pdb file of my sytem and added their corresponding atomtypes, bondtypes, dihedrals and forcefield parameters in oplsaa.ff directory. but still facing problem while using pdb2gmx command.  
Also i want to know what is the difference between “ATOM” and HETATM. because in both case i found different erors.  
waiting fir your kind response.

 ![error while using HETATM](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/8/810562087df30645531d3725a447b73daf4bafb2.png)

all screenshots of errors and pdb file is attached herewith.  
Please help me in finding problem

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<div class="post-metadata">

**Author:** ![saiqa](https://avatars.discourse-cdn.com/v4/letter/s/b19c9b/32.png) [@saiqa](https://gromacs.bioexcel.eu/u/saiqa)\
**Post date:** [September 8, 2022, 12:39pm UTC](https://gromacs.bioexcel.eu/t/problem-in-generating-topology-file-of-a-polymer/4757/2 "2022-09-08T12:39:54Z")

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![aminoacid.rtp file](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/0/0204c6f14bfce450ef225c5abada2fce2ab295a4.png)  
this is my .rtp file.

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<div class="post-metadata">

**Author:** ![nano](https://avatars.discourse-cdn.com/v4/letter/n/dec6dc/32.png) [@nano](https://gromacs.bioexcel.eu/u/nano)\
**Post date:** [September 8, 2022, 7:45pm UTC](https://gromacs.bioexcel.eu/t/problem-in-generating-topology-file-of-a-polymer/4757/3 "2022-09-08T19:45:29Z")

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There are multiple issues with your residue definition.

- The error indicated that “OXY” is one taken name, so you need to use other names.

- The definition of the residue lacks bonding information through neighboring residues.

For your reference, here is my example (the focus here is the bonding in the residue definition while the other is just an example, NOT for research).

```auto
[PEO1]
 [atoms]

;CH3
C31 opls_181 0.11 1
HP1 opls_185 0.03 1
HP2 opls_185 0.03 1
HP3 opls_185 0.03 1

;O
OP1 opls_180 -0.40 1
           
;CH2            
C21 opls_182 0.14 1
HP4 opls_185 0.03 1
HP5 opls_185 0.03 1
           
;CH2            
C22 opls_182 0.14 1
HP6 opls_185 0.03 1
HP7 opls_185 0.03 1

 
 [bonds]
HP1 C31
HP2 C31
HP3 C31
C31 OP1
OP1 C21
C21 HP4
C21 HP5
C21 C22
C22 HP6
C22 HP7
C22 +OP1

 [angles]

 
[PEO2]
 [atoms]
;O          
OP1 opls_180 -0.40 1
           
;CH2            
C21 opls_182 0.14 1
HP1 opls_185 0.03 1
HP2 opls_185 0.03 1
           
;CH2            
C22 opls_182 0.14 1
HP3 opls_185 0.03 1
HP4 opls_185 0.03 1

 
 [bonds]
-C22 OP1
OP1 C21
C21 HP1
C21 HP2
C21 C22
C22 HP3
C22 HP4
C22 +OP1

 [angles]

 
[PEO3]
 [atoms]
;O          
OP1 opls_180 -0.40 1
           
;CH2            
C21 opls_182 0.14 1
HP1 opls_185 0.03 1
HP2 opls_185 0.03 1
           
;CH2            
C22 opls_182 0.14 1
HP3 opls_185 0.03 1
HP4 opls_185 0.03 1
           
;O          
OP2 opls_180 -0.40 1
           
;CH3            
C31 opls_181 0.11 1
HP5 opls_185 0.03 1
HP6 opls_185 0.03 1
HP7 opls_185 0.03 1

 
 [bonds]
-C22 OP1
OP1 C21
C21 HP1
C21 HP2
C21 C22
C22 HP3
C22 HP4
C22 OP2
OP2 C31
C31 HP5
C31 HP6
C31 HP7

 [angles]

```

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<div class="post-metadata">

**Author:** ![saiqa](https://avatars.discourse-cdn.com/v4/letter/s/b19c9b/32.png) [@saiqa](https://gromacs.bioexcel.eu/u/saiqa)\
**Post date:** [September 9, 2022, 2:00am UTC](https://gromacs.bioexcel.eu/t/problem-in-generating-topology-file-of-a-polymer/4757/4 "2022-09-09T02:00:11Z")

</div>

Thanks dear for your kind response.  
Can you share an exemplary pdb file also for which you just define the above residues. it will be more helpfully to clear the concepts behind such arrangements.  
waiting for your kind response.  
Regards

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<div class="post-metadata">

**Author:** ![saiqa](https://avatars.discourse-cdn.com/v4/letter/s/b19c9b/32.png) [@saiqa](https://gromacs.bioexcel.eu/u/saiqa)\
**Post date:** [September 9, 2022, 2:17am UTC](https://gromacs.bioexcel.eu/t/problem-in-generating-topology-file-of-a-polymer/4757/5 "2022-09-09T02:17:41Z")

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actually I had defined a polymer into 3 parts (Terminal1 with residue name HYD, repeating unit C2H4O with residue name ETO and Terminal 2 with residue name OXY)  
the problem is how and where the bond joining terminal 1 to repeating unit and repeating unit to terminal 2 must be defined

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<div class="post-metadata">

**Author:** ![nano](https://avatars.discourse-cdn.com/v4/letter/n/dec6dc/32.png) [@nano](https://gromacs.bioexcel.eu/u/nano)\
**Post date:** [September 9, 2022, 1:35pm UTC](https://gromacs.bioexcel.eu/t/problem-in-generating-topology-file-of-a-polymer/4757/6 "2022-09-09T13:35:11Z")

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Here it is. But you do not have to have the same name as mine. And also the definition is not unique (You can also define it whatever way you like).

```auto
TITLE PEO
ATOM 1 C31 PEO1 1 -0.034 -1.337 0.010 1.00 0.00 C
ATOM 2 HP1 PEO1 1 -0.289 -2.093 -0.761 1.00 0.00 H
ATOM 3 HP2 PEO1 1 -0.862 -0.594 0.033 1.00 0.00 H
ATOM 4 HP3 PEO1 1 0.049 -1.879 0.979 1.00 0.00 H
ATOM 5 OP1 PEO1 1 1.180 -0.718 -0.352 1.00 0.00 O
ATOM 6 C21 PEO1 1 1.640 0.090 0.713 1.00 0.00 C
ATOM 7 HP4 PEO1 1 2.217 -0.527 1.435 1.00 0.00 H
ATOM 8 HP5 PEO1 1 0.801 0.600 1.247 1.00 0.00 H
ATOM 9 C22 PEO1 1 2.528 1.200 0.162 1.00 0.00 C
ATOM 10 HP6 PEO1 1 2.841 1.839 1.018 1.00 0.00 H
ATOM 11 HP7 PEO1 1 1.906 1.791 -0.550 1.00 0.00 H
ATOM 12 OP1 PEO2 2 3.664 0.656 -0.488 1.00 0.00 O
ATOM 13 C21 PEO2 2 4.459 1.700 -1.026 1.00 0.00 C
ATOM 14 HP1 PEO2 2 4.871 1.375 -2.005 1.00 0.00 H
ATOM 15 HP2 PEO2 2 3.867 2.619 -1.257 1.00 0.00 H
ATOM 16 C22 PEO2 2 5.602 2.079 -0.077 1.00 0.00 C
ATOM 17 HP3 PEO2 2 5.186 2.338 0.918 1.00 0.00 H
ATOM 18 HP4 PEO2 2 6.083 3.021 -0.423 1.00 0.00 H
ATOM 19 OP1 PEO2 3 6.532 1.016 0.084 1.00 0.00 O
ATOM 20 C21 PEO2 3 7.532 1.049 -0.925 1.00 0.00 C
ATOM 21 HP1 PEO2 3 7.721 2.069 -1.334 1.00 0.00 H
ATOM 22 HP2 PEO2 3 7.240 0.385 -1.767 1.00 0.00 H
ATOM 23 C22 PEO2 3 8.874 0.597 -0.354 1.00 0.00 C
ATOM 24 HP3 PEO2 3 9.135 1.263 0.502 1.00 0.00 H
ATOM 25 HP4 PEO2 3 9.627 0.707 -1.169 1.00 0.00 H
ATOM 26 OP1 PEO3 4 8.803 -0.752 0.054 1.00 0.00 O
ATOM 27 C21 PEO3 4 10.046 -1.148 0.610 1.00 0.00 C
ATOM 28 HP1 PEO3 4 10.921 -0.645 0.131 1.00 0.00 H
ATOM 29 HP2 PEO3 4 10.050 -0.921 1.699 1.00 0.00 H
ATOM 30 C22 PEO3 4 10.242 -2.645 0.407 1.00 0.00 C
ATOM 31 HP3 PEO3 4 9.407 -3.187 0.904 1.00 0.00 H
ATOM 32 HP4 PEO3 4 11.213 -2.917 0.886 1.00 0.00 H
ATOM 33 OP2 PEO3 4 10.256 -2.927 -0.977 1.00 0.00 O
ATOM 34 C31 PEO3 4 10.685 -4.253 -1.183 1.00 0.00 C
ATOM 35 HP5 PEO3 4 11.764 -4.364 -0.938 1.00 0.00 H
ATOM 36 HP6 PEO3 4 10.565 -4.496 -2.259 1.00 0.00 H
ATOM 37 HP7 PEO3 4 10.062 -4.982 -0.618 1.00 0.00 H
END

```

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<div class="post-metadata">

**Author:** ![saiqa](https://avatars.discourse-cdn.com/v4/letter/s/b19c9b/32.png) [@saiqa](https://gromacs.bioexcel.eu/u/saiqa)\
**Post date:** [September 10, 2022, 3:39am UTC](https://gromacs.bioexcel.eu/t/problem-in-generating-topology-file-of-a-polymer/4757/7 "2022-09-10T03:39:04Z")

</div>

Thanks for your kind reply and sharing yor PDB. The idea which i got from your pdb and .rtp file is you define the whole monomer attached to terminal as a terminal residue defining the terminals for polymer chain. Got it.  
can i ask one other help?  
I had changed my pdb and .rtp according to you suggested in last response. Now gromacs can read my pdb. But this time it is showing error in reading hydrogens. It says I should define hydrogens of my peo chain in aminoacids.hdb.  
can you share a sample of that also.

I am attaching mine and i know it was wrong because gromacs is showing error while reading it. waiting for your kind response.

Regards,  
Saiqa

 ![Screenshot from 2022-09-09 21-26-29.png](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/5/59b445eace1124bd7941aa58c46bdeee55ce2d47.png)

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<div class="post-metadata">

**Author:** ![nano](https://avatars.discourse-cdn.com/v4/letter/n/dec6dc/32.png) [@nano](https://gromacs.bioexcel.eu/u/nano)\
**Post date:** [September 12, 2022, 5:05pm UTC](https://gromacs.bioexcel.eu/t/problem-in-generating-topology-file-of-a-polymer/4757/8 "2022-09-12T17:05:44Z")

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I’m not sure, unfortunately. It said error reading that file, but I did not encounter the same problem before.

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<div class="post-metadata">

**Author:** ![sumanc](https://avatars.discourse-cdn.com/v4/letter/s/b3f665/32.png) [@sumanc](https://gromacs.bioexcel.eu/u/sumanc)\
**Post date:** [September 21, 2022, 5:12pm UTC](https://gromacs.bioexcel.eu/t/problem-in-generating-topology-file-of-a-polymer/4757/9 "2022-09-21T17:12:29Z")

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A good place to start:  
[https://manual.gromacs.org/current/reference-manual/topologies/pdb2gmx-input-files.html](https://manual.gromacs.org/current/reference-manual/topologies/pdb2gmx-input-files.html)

Read the section “Hydrogen database”.

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<div class="post-metadata">

**Author:** ![saiqa](https://avatars.discourse-cdn.com/v4/letter/s/b19c9b/32.png) [@saiqa](https://gromacs.bioexcel.eu/u/saiqa)\
**Post date:** [September 21, 2022, 5:28pm UTC](https://gromacs.bioexcel.eu/t/problem-in-generating-topology-file-of-a-polymer/4757/10 "2022-09-21T17:28:40Z")

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Thanks for sharing it. I had also tried accordingly but no result  
After that thoroughly understanding your pdb file and sequence to define hydrogens has solved my problem. For that i am still thankful to you.

Best Regards,  
Saiqa