CHARMM Development Project
Posted By: hasan mahmud Patching of Glycine to hydroxyproline - 07/09/18 02:35 PM
Hi All,
Good day! I am working with collagen molecule that has engineered residue hydroxyproline (HYP). While I am trying to generate psf file by CHARMM-GUI website HYP residue is detected as engineered residue and deleted from the data of structure file. I believe in the rtf file topology of HYP is absent that causes the problem.

So I have tried to generate topology of HYP by swissparam website, they generated it successfully, however when I am adding the topology information of HYP to the original rtf file and tried to build psf file of full collagen model by VMD, HYP residue is not patching with GLY residue.

I believe main problem with patching of HYP with GLY. I have attached my topology file for your evaluation. Can you please see the file and if you find what causes the problem will be appreciated, helpful for my research?


Description: Topology file HYP
Attached File
top_all36_prot.txt  (255 downloads)
Posted By: rmv Re: Patching of Glycine to hydroxyproline - 07/09/18 03:09 PM
VMD questions should be direction to the VMD/NAMD people.

I do not recommend the use of the SwissParam site; the charge methodology is different from that used in CHARMM FF development.

There is a separate forum for issues related to CHARMM-GUI.

The HYP residue appears to use chemical types that are not defined in the MASS statements, so there will be issues.

I suggest creating a minimal modification of the existing PRO residue, after submitting a hydroxyproline analog to the ParamChem server to evaluate the charges and force constants needed to add the -OH group. This is the approach recommended in posts here in this forum, and supporting documents, for adding molecules that are (mostly) already described in the force field.
Posted By: alex Re: Patching of Glycine to hydroxyproline - 07/15/18 08:54 PM
Hello,

RESI HYP is available.

prot/toppar_all36_prot_modify_res.str:RESI HYP 0.00 ! hydroxyproline

I'm not sure why the CHARMM-GUI doesn't find it, but treat the residue as PRO, download the inputs created by the CHARMM-GUI and modify them to use HYP rather the PRO.

alex
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