are you sure that you want to be using both ntr=1 and nmropt=1? they are
different types of restraints, and it's possible to use both but you need
to take extra care.
On Tue, Jan 25, 2022 at 10:16 AM Prithviraj Nandigrami <
prithviraj.nandigrami.einsteinmed.edu> wrote:
> Hi,
>
> Here is the complete input file I am trying to run:
>
> Hi,
>
> Sorry about my ommision.
>
> Here is the input file:
>
> simann with pos-restraint on receptor + dist restraint on ligand
> &cntrl
> ntwx = 100,
> ntwe = 100, ntwr = 50, ntpr = 1000, ntxo = 1, ioutfm = 0,
> imin = 0,
> ntx = 1,
> temp0 = 300,
> tempi = 300,
> ig = -1,
> nstlim = 20000,
> dt = 0.002,
> ntb = 0,
> nscm = 100,
> ntc = 2, ntf = 2,
> ntt = 2, vrand = 1000,
> igb = 1, cut = 999.0,
> nmropt = 1,
> ntr = 1,
> /
> &wt type='END', /
> DISANG=./restraints.in
>
> ________________________________
> From: Rana Rehan Khalid <ray.binm.gmail.com>
> Sent: Tuesday, January 25, 2022 10:12 AM
> 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: David A Case <david.case.rutgers.edu<mailto:david.case.rutgers.edu>>
> Date: Tue, Jan 25, 2022 at 9:06 AM
> Subject: Re: [AMBER] Restraint file for amber20 with pmemd.cuda
> implementation
> To: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
>
>
> On Mon, Jan 24, 2022, Prithviraj Nandigrami wrote:
>
> >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<
> https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Frestraints.in%2F&data=04%7C01%7Cprithviraj.nandigrami%40einsteinmed.edu%7C7e2a7af6f6824bd1705208d9e015230a%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637787203658556243%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=g09iGQTmDOuekWO%2FFTCzyjbMi%2BKaTjuM4JK33D86QKs%3D&reserved=0
> >
> >
> > rfree: End of file on unit 5
>
> This error has nothing to do with the restraint block you posted. Can you
> post the complete mdin file? The program thinks your "DISANG" card is the
> title for a set of group restraints, which suggests that you have something
> in the wrong place.
>
> It's possible that an input file that worked in Amber12 might fail in
> Amber20, but we need to get more information.
>
> ....dac
>
>
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Received on Tue Jan 25 2022 - 07:30:02 PST
