Tutorial-l Mailing List

From: 대학원/일반대학원 생명과학부 (ihc0213_at_yonsei.ac.kr)
Date: Mon Dec 10 2018 - 19:58:16 CST

Dear All NAMD users,

Hello,
I tried to test FEP in NAMD and make files from VMD.

In namd simulation, I got error message like this.

FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT

I know that this problem is related with parameters in CHARMM36,
and there is a parameter 'OT' in CHARMM27, but isn't in CHARMM36.

I read some comments that I have to patch my psf file in VMD.

What should I do for 'the patch'?

Although there is 'Add patch' in VMD,
I don't know what 'Patch type', 'Segment 1', and so on are.

Please let me know how I patch my files correctly.

Thank you!

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