Dear David, Shahid and AMBER users,
thank you for the advices but now
this error occured again:
************************************
Here is the input file:
initial minimization solvent +
ions
&cntrl
imin =
1,
maxcyc =
4000,
ncyc =
2000,
ntb =
1,
ntr =
1,
cut =
12.0
restraint_wt=100,
restraintmask='.P,OP1,OP2,O5',C5',H5',H5'',C4',H4',O4',C1',H1',C3',H3',C2',H2',H2'',O3'',HOP3,OP3',
/
error in reading namelist cntrl
**********************************************************
The input file was:
initial minimization solvent +
ions
&cntrl
imin =
1,
maxcyc =
4000,
ncyc =
2000,
ntb =
1,
ntr =
1,
cut =
12.0
restraint_wt=100,
restraintmask='.P,OP1,OP2,O5',C5',H5',H5'',C4',H4',O4',C1',H1',C3',H3',C2',H2',H2'',O3'',HOP3,OP3',
/
with the blank line after /.
The blank line above &cntrl did not help either.
It seems like the sander takes the first apostrophe after . (in O5') for
the end of the restraintmask input,
since restraintmask='.P,OP1,OP2' did work.
Thank you in advance,
Nick
Message: 3
Date: Wed, 14 Mar 2018 16:09:39 -0400
From: David A Case <david.case.rutgers.edu>
Subject: Re: [AMBER] restraintmask, error in reading namelist cntrl
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<20180314200939.heq5ewfagvvuckh6.vpn-client-172-16-8-64.rutgers.edu>
Content-Type: text/plain; charset=us-ascii
On Wed, Mar 14, 2018, Nikolay N. Kuzmich wrote:
> restraintmask='.{P, OP1, OP2, O5', C5', H5', H5'', C4', H4', O4', C1',
> H1', C3', H3', C2', H2', H2'', O3'', HOP3, OP3}'
Leave out the spaces and the "{","}" characters:
restraintmask='.P,OP1,OP2,O5',C5',H5',H5'',C4',H4',O4',C1',
H1',C3',H3',C2',H2',H2'',O3'',HOP3,OP3',
(All on one line).
...dac
Message: 9
Date: Wed, 14 Mar 2018 16:51:25 +0100
From: "Dr. M. Shahid" <mohammad.shahid.gmail.com>
Subject: Re: [AMBER] restraintmask, error in reading namelist cntrl
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CABa5kwNGnb2PPMy3tjNG96=dHzzJ0L73JesqTeEQGrB04-bgzQ.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Hi,
you need to insert a blank new line before &cntrl and then try again.
HTH,
--
Shahid.
On Wed, Mar 14, 2018 at 4:10 PM, Nikolay N. Kuzmich <nnkuzmich.gmail.com>
wrote:
> Dear Amber users and developers,
>
> when running restrained minimization
> I receive error message "error in reading namelist cntrl".
> Is the error in restraintmask syntaxis or somewhere else?
> The input is:
>
> minimization with backbone restrained
> &cntrl
> imin=1,
> maxcyc=4000,
> ncyc=2000,
> ntb=1,
> ntr=1,
> cut=12.0,
> restraint_wt=100.0,
> restraintmask='.{P, OP1, OP2, O5', C5', H5', H5'', C4', H4', O4', C1',
> H1', C3', H3', C2', H2', H2'', O3'', HOP3, OP3}'
> /
>
> Thank you in advance,
> Nick
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Received on Fri Mar 16 2018 - 09:00:02 PDT
