# Multiple topology and parameter file in run.cns

**URL:** <https://ask.bioexcel.eu/t/multiple-topology-and-parameter-file-in-run-cns/2344>\
**Category:** HADDOCK\
**Created:** [July 20, 2020, 5:50pm UTC](https://ask.bioexcel.eu/t/multiple-topology-and-parameter-file-in-run-cns/2344 "2020-07-20T17:50:35Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![mitradip](https://avatars.discourse-cdn.com/v4/letter/m/6f9a4e/32.png) [@mitradip](https://ask.bioexcel.eu/u/mitradip)\
**Post date:** [July 20, 2020, 5:50pm UTC](https://ask.bioexcel.eu/t/multiple-topology-and-parameter-file-in-run-cns/2344/1 "2020-07-20T17:50:35Z")

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I have a protein which I want to dock with a peptide, but the protein has N-Acetyl-Glucopyranose. I changes the residue name to GLP and I also have the parameters in glycans-uu.top and glycans-uu.param.

However, I should ideally modify the run.param or run.cns to include the parameters. However, when I try the following statements:

{===================== topology and parameter files ======================}

{\* topology file for molecule 1 _}  
{===\>} prot\_top\_mol1=“protein-allhdg5-4.top glycans-uu.top”;  
{_ topology file for molecule 2 \*}  
{===\>} prot\_top\_mol2=“protein-allhdg5-4.top”;

OR

{===================== topology and parameter files ======================}

{\* topology file for molecule 1 _}  
{===\>} prot\_top\_mol1=“protein-allhdg5-4.top,glycans-uu.top”;  
{_ topology file for molecule 2 \*}  
{===\>} prot\_top\_mol2=“protein-allhdg5-4.top”;

I get same error message, i.e. it cannot find the GLP residue in my system, however, GLP is present in glycans-uu.top and glycans-uu.param file. I cannot remove protein-allhdg5-4.top and protein-allhdg5-4.param as it contains parameters for proteins. However, it seems I cannot include multiple files topology files, though it seems including multiple topology files will solve the issue.

Hence, can anyone provide me a bit of assistance about this issue?

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<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:** [July 20, 2020, 8:47pm UTC](https://ask.bioexcel.eu/t/multiple-topology-and-parameter-file-in-run-cns/2344/2 "2020-07-20T20:47:31Z")

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If you have the latest version of HADDOCK (2.4-July-2020) N-acetyl glucopyranose “should be” supported (no changes in topo/param files required in run.cns. The residue should however be properly named. The supported glucopyranose are:

- NDG: 2-N-acetyl-alpha-D-glucopyranose
- A2G: 2-N-acetyl-alpha-D-glucopyranose, different stereochemistry at C4
- NAG: 2-N-acetyl-beta-D-glucopyranose

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<div class="post-metadata">

**Author:** ![mitradip](https://avatars.discourse-cdn.com/v4/letter/m/6f9a4e/32.png) [@mitradip](https://ask.bioexcel.eu/u/mitradip)\
**Post date:** [July 21, 2020, 4:14am UTC](https://ask.bioexcel.eu/t/multiple-topology-and-parameter-file-in-run-cns/2344/3 "2020-07-21T04:14:36Z")

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Hi,

Thank you so much for the suggestion.

However, replacing with NAG and including only the protein-allhdg5-4.top gives an error. The error is as follows:

> %GENRES-ERR: residue NAG not found in topology files. Add topology definition.

Can you kindly let me know about the issue? Is it a feature available only in Haddock2.4-July2020? I am using its just previous version, Haddock2.4-June2020.

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<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:** [July 21, 2020, 6:38am UTC](https://ask.bioexcel.eu/t/multiple-topology-and-parameter-file-in-run-cns/2344/4 "2020-07-21T06:38:49Z")

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Yes you do need the July version as I explained.

Send me an email