AMBER Archive (2006)

Subject: Re: AMBER: NMR restraint

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Fri Jun 02 2006 - 14:23:28 CDT

When I run it with anothe format of namelist of dist file,
I've got another errore message

===============================
 Here are comments from the DISANG input file:
 # membrane distance restraints

 Error: Too many atom ranges need to be stored for center-of-mass distance
        restraints. MAXGRP = 4. This needs to be increased.
=========================

Now, MAXGRP is 4.

Only difference is format.

On 6/2/06, Myunggi Yi <myunggi_at_gmail.com> wrote:
> When I run it on another machine, I've got the following message
>
> =====================
> Here are comments from the DISANG input file:
> # membrane distance restraints
>
> Error: Too many atom ranges need to be stored for center-of-mass distance
> restraints. MAXGRP = 6. This needs to be increased.
>
> =====================
>
> I don't understand this error message.
> I have only 34 atoms. According to the manual,
> I should be able to include up to 200 atoms.
>
> Is this a bug?
>
>
> On 6/2/06, Myunggi Yi <myunggi_at_gmail.com> wrote:
> > Dear Amber users,
> >
> > In order to keep the thickness of membrane bilayers,
> > I'm using average distance NMR restraints.
> >
> > I've got the following output
> >
> > ======= the output file ========
> > Begin reading energy term weight changes/NMR restraints
> > WEIGHT CHANGES:
> > ** No weight changes given **
> >
> > RESTRAINTS:
> > Requested file redirections:
> > DISANG = dist
> > Restraints will be read from file: dist
> > Here are comments from the DISANG input file:
> > # membrane distance restraints
> >
> >
> > ==========================
> >
> > and error message from the job manager
> >
> > ==================
> > 1525-049 The list-directed or NAMELIST READ statement cannot be
> > completed because the input data did not specify a valid delimited
> > character string. The program will recover by ignoring the item in
> > the READ statement.
> > 1525-049 The list-directed or NAMELIST READ statement cannot be
> > completed because the input data did not specify a valid delimited
> > character string. The program will recover by ignoring the item in
> > the READ statement.
> > 1525-049 The list-directed or NAMELIST READ statement cannot be
> > completed because the input data did not specify a valid delimited
> > character string. The program will recover by ignoring the item in
> > the READ statement.
> > 1525-049 The list-directed or NAMELIST READ statement cannot be
> > completed because the input data did not specify a valid delimited
> > character string. The program will recover by ignoring the item in
> > the READ statement.
> > ==================
> >
> > My input file is
> >
> > ======= input file =============
> > minimization with membrane thickness restraint
> > &cntrl
> >
> > imin=1, irest=0, maxcyc=800, ncyc=100
> >
> > ntpr=100, cut=9.0, nsnb=10,
> >
> > ntb=1, ntrx=1,
> >
> > ntc=1, nmropt=1,
> > &end
> > &end
> > &wt type='END'
> > &end
> > DISANG=dist
> > ==========================
> >
> > and NMR restraint
> >
> > ====== file dist ===============
> > # membrane distance restraints
> > &rst iat=-1,-1, iresid=1,
> > r1=20.0, r2=35.0, r3=35.0, r4=50.0,
> > rk2=5.0, rk3=5.0,
> > igr1 = 4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,
> > 21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,0,
> > grnam1(1)='P',grnam1(2)='P',grnam1(3)='P',grnam1(4)='P',grnam1(5)='P',
> > grnam1(6)='P',grnam1(7)='P',grnam1(8)='P',grnam1(9)='P',grnam1(10)='P',
> > grnam1(11)='P',grnam1(12)='P',grnam1(13)='P',grnam1(14)='P',grnam1(15)='P',
> > grnam1(16)='P',grnam1(17)='P',grnam1(18)='P',grnam1(19)='P',grnam1(20)='P',
> > grnam1(21)='P',grnam1(22)='P',grnam1(23)='P',grnam1(24)='P',grnam1(25)='P',
> > grnam1(26)='P',grnam1(27)='P',grnam1(28)='P',grnam1(29)='P',grnam1(30)='P',
> > grnam1(31)='P',grnam1(32)='P',grnam1(33)='P',grnam1(34)='P',
> > # grnam1='P','P','P','P','P','P','P','P','P','P','P','P','P','P','P',
> > # 'P','P','P','P','P','P','P','P','P','P','P','P','P','P','P',
> > # 'P','P','P','P',
> > igr2 = 2,3,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,
> > 54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,0,
> > grnam2(1)='P',grnam2(2)='P',grnam2(3)='P',grnam2(4)='P',grnam2(5)='P',
> > grnam2(6)='P',grnam2(7)='P',grnam2(8)='P',grnam2(9)='P',grnam2(10)='P',
> > grnam2(11)='P',grnam2(12)='P',grnam2(13)='P',grnam2(14)='P',grnam2(15)='P',
> > grnam2(16)='P',grnam2(17)='P',grnam2(18)='P',grnam2(19)='P',grnam2(20)='P',
> > grnam2(21)='P',grnam2(22)='P',grnam2(23)='P',grnam2(24)='P',grnam2(25)='P',
> > grnam2(26)='P',grnam2(27)='P',grnam2(28)='P',grnam2(29)='P',grnam2(30)='P',
> > grnam2(31)='P',grnam2(32)='P',grnam2(33)='P',grnam2(34)='P',
> > # grnam2='P','P','P','P','P','P','P','P','P','P','P','P','P','P','P',
> > # 'P','P','P','P','P','P','P','P','P','P','P','P','P','P','P',
> > # 'P','P','P','P',
> > &end
> > ==============================
> >
> > As you see, at first time I tried "grnam2='P','P','P','P',....." format.
> > I've got the same result.
> > Is there anything wrong in my input files?
> >
> >
> > --
> > Best wishes,
> >
> > MYUNGGI YI
> > ==================================
> > KLB 419
> > Institute of Molecular Biophysics
> > Florida State University
> > Tallahassee, FL 32306
> >
> > Office: (850) 645-1334
> > http://www.scs.fsu.edu/~myunggi
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
>
>
> --
> Best wishes,
>
> MYUNGGI YI
> ==================================
> KLB 419
> Institute of Molecular Biophysics
> Florida State University
> Tallahassee, FL 32306
>
> Office: (850) 645-1334
> http://www.scs.fsu.edu/~myunggi
> 

-- 
Best wishes,

MYUNGGI YI
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
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