Tutorial-l Mailing List

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Tue Dec 11 2018 - 09:17:20 CST

Hi,

did you include the toppar_water_ions.str file in your simulation? The "OT"
atom is the TIP3P oxygen. If that is not the case, you will need to provide
more information about your system.

Regarding your patch, I believe that there might be some confusion on what
a patch means, and probably the comments that you read don't apply to your
case. Anyway, I would suggest you to go through the namd tutorial as
introductory material as the free-energy method tutorials assume that you
are already comfortable running simulations in NAMD.

Best

João

On Mon, Dec 10, 2018 at 7:58 PM ­임호철(대학원/일반대학원 생명과학부(생명공학)) <
ihc0213_at_yonsei.ac.kr> wrote:

> 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!
> 

-- 
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
http://www.ks.uiuc.edu/~jribeiro/
jribeiro_at_ks.uiuc.edu
+1 (217) 3005851
**
** Visit http://www.greatcircle.com/majordomo/ for more info on majordomo
**