Yes, I tried this input file with amber20 (using the executable pmemd.cuda on a graphics card) and got an error message. Specifically, I get the following in the output log file:
5. REFERENCE ATOM COORDINATES
default_name
----- READING GROUP 1; TITLE:
DISANG=./restraints.in
rfree: End of file on unit 5
Any insight on how to fix this error would be much appreciated.
Thank you.
P.N.
________________________________
From: Rana Rehan Khalid <ray.binm.gmail.com>
Sent: Monday, January 24, 2022 5:09 PM
To: Prithviraj Nandigrami <prithviraj.nandigrami.einsteinmed.edu>
Subject: Fwd: [AMBER] Restraint file for amber20 with pmemd.cuda implementation
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---------- Forwarded message ---------
From: Carlos Simmerling <carlos.simmerling.gmail.com<mailto:carlos.simmerling.gmail.com>>
Date: Mon, Jan 24, 2022 at 4:47 PM
Subject: Re: [AMBER] Restraint file for amber20 with pmemd.cuda implementation
To: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
did you try this in Amber 20 and get an error? with a quick glance it seems
ok.
On Mon, Jan 24, 2022 at 4:31 PM Prithviraj Nandigrami <
prithviraj.nandigrami.einsteinmed.edu<mailto:prithviraj.nandigrami.einsteinmed.edu>> wrote:
> Dear All,
>
> I am trying to setup an MD run with distance restraint between two atoms.
> My restraint file for amber12 looks as below:
>
> # LIG119.CA<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Flig119.ca%2F&data=04%7C01%7Cprithviraj.nandigrami%40einsteinmed.edu%7C2f14bd1cd74948d6a51008d9df8637a1%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637786589838737851%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=wKhsyc9g4hINB5JfZso2vuja%2Fk8PVqVDqdYub%2FKPepU%3D&reserved=0> DUM120.D1
> &rst
> iat=1758,1774,
> ialtd=0,
> r1= 0, r2= 0.1, r3= 15, r4= 15.1,
> rk2=500.0, rk3=500.0 ,
> /
>
>
> How do I convert this restraint file to be compatible with amber20 using
> pmemd.cuda?
>
> Any help would be much appreciated.
>
> Thank you.
> P. N.
>
>
>
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Received on Mon Jan 24 2022 - 14:30:03 PST
