AMBER Archive (2006)

Subject: Re: AMBER: NMR restraint

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Fri Jun 02 2006 - 14:15:41 CDT

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
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> 

-- 
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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