Hi,
as I'm having lot of fun with this my last simulation, I'll show you my results following your suggests (adding commas, taking out blank spaces and using group restraints too), but it's been for days now that I'm receiving the last error text (the best one in my opinion):
nstlim = 500000, dt = 0.002,
ioutfm=1, iwrap=1,
ntpr=500, ntwx=500, ntwr=1000,
restraintmask=':1639, 1642, 1645, 1648',
restraint_wt=1.0
vlimit=2.0, nmropt=1,
/
&wt type='END'
/
Hold Fe4S4
50.0
RES 1639 1648
END
END
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
** No weight changes given **
RESTRAINTS:
No valid redirection requests found
ioutfm=1, iwrap=1,
ntpr=500, ntwx=500, ntwr=1000,
restraintmask=':1639, 1642, 1645, 1648',
restraint_wt=1.0
vlimit=2.0
/
&wt type='END'
/
Hold Fe4S4
50.0
RES 1639 1648
END
END
| ERROR: PMEMD does not support intermolecular PRFs!
tempi=300.0, temp0=300.0,
ntt=3, ig=-1, gamma_ln=1.0,
nstlim = 500000, dt = 0.002,
ioutfm=1, iwrap=1,
ntpr=500, ntwx=500, ntwr=1000,
/
&wt type='END'
/
Hold Fe4S4
50.0
RES 1639 1648
END
END
----- READING GROUP 1; TITLE:
Hold Fe4S4
GROUP 1 HAS HARMONIC CONSTRAINTS 50.00000
GRP 1 RES 1639 TO 1648
Number of atoms in this group = 182
----- READING GROUP 2; TITLE:
END
GROUP 2 HAS HARMONIC CONSTRAINTS 0.00000
rfree: End of file on unit 5
tempi=300.0, temp0=300.0,
ntt=3, ig=-1, gamma_ln=1.0,
nstlim = 500000, dt = 0.002,
ioutfm=1, iwrap=1,
ntpr=500, ntwx=500, ntwr=1000
/
Hold Fe4S4
50.0
RES 1639 1648
END
END
default_name
----- READING GROUP 1; TITLE:
Hold Fe4S4
GROUP 1 HAS HARMONIC CONSTRAINTS 50.00000
GRP 1 RES 1639 TO 1648
Number of atoms in this group = 182
----- READING GROUP 2; TITLE:
END
GROUP 2 HAS HARMONIC CONSTRAINTS 0.00000
rfree: End of file on unit 5
Do you users think that might be a problem with my system? Minimization and heating step went right, but I don't know what else think
Many many thanks
Damiano
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: 13 September 2015 04:12
To: AMBER Mailing List
Subject: Re: [AMBER] No output
On Sat, Sep 12, 2015 at 5:02 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Damiano,
>
> The relevant error is this one:
>
> At line 463 of file mdin_ctrl_dat.F90 (unit = 5, file = 'LAMPLP_MD2.in')
> Fortran runtime error: Cannot match namelist object name restraint_mask
> You are using PMEMD v12 and if memory serves (don't have the code or
> manual in front of me right now) the restraint_mask input approach is not
> supported in that version of pmemd - you have to use the more traditional
> group based input.
>
​Actually, I think it does. I added support for restraint masks when I was
at UCSD in spring 2011 (I know it was before the summer of 2011, so it
*should* be in Amber 12).
The problem is that the variable is "restraintmask", not "restraint_mask".
The variables are "restraintmask" and "restraint_wt" for cartesian
restraints.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 14 2015 - 06:00:09 PDT
