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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Received on Sun Jun 04 2006 - 06:07:16 PDT
