[AMBER] Various Errors in Tests

From: Philipp Marquetand <philipp.marquetand.ens.fr>
Date: Tue, 9 Mar 2010 11:45:28 +0100

Hi,

cd rdc && ./Run.dip
and
cd noesy && ./Run.noesy
terminate with Program error

tail of gcg.dip.o:

  RESTRAINTS:
  Requested file redirections:
   LISTOUT = POUT
   DISANG = RST.allang
   DIPOLE = RST.dip
   SHIFTS = gcg10.shf
  Restraints will be read from file: RST.allang
Here are comments from the DISANG input file:
#
# 1 GUA H1' 1 GUA H3' 4.6

  ERROR: r1 -> r4 (and r1a -> r4a) must be monotonically increasing;
Offending restraint:
******
  H3' ( 27)-H2'1( 29) NSTEP1= 0
NSTEP2= 0
R1 = 6.500 R2 = 6.500 R3 = 3.400 R4 = 3.400 RK2 = 0.000 RK3
= 32.000

tail of noesy.out:

  RESTRAINTS:
  Requested file redirections:
   NOESY = NXP.8May95
   DISANG = RST.16sept93
   LISTOUT = POUT
  Restraints will be read from file: RST.16sept93
Here are comments from the DISANG input file:
#
# 1 GUA h1p 1 GUA h2d 2.7 (#141

  ERROR: r1 -> r4 (and r1a -> r4a) must be monotonically increasing;
Offending restraint:
******
  H2'2( 30)-H2'1( 59) NSTEP1= 0
NSTEP2= 0
R1 = 5.800 R2 = 5.800 R3 = 4.800 R4 = 4.800 RK2 = 0.000 RK3
= 32.000



mdout.tip5p.save has in the section
       R M S F L U C T U A T I O N S
the following additional lines
  EKCMT = 0.2952 VIRIAL = 9.6699 VOLUME
= 0.0001
                                                     Density
= 0.0000
So, the fluctuations of these values are not calculated anymore?
Why less functionality?

jar gives completely different results
first lines of mdout.jar.dif:
87c87
< R1 = -85.000 R2 = 15.000 R3 = 15.000 R4 = 115.000 RK2 =5000.000
RK3 = 5000.000
---
 > R1 = 115.000 R2 = 115.000 R3 = 115.000 R4 = 115.000 RK2 =5000.000  
RK3 = 5000.000
same for plane_plane_restraint:
first lines of dout.dinucAU_plpt.dif
97,98c97,98
< R1 =   0. R2 =   5.000 R3 =   5.000 R4 = 505.000 RK2 =   3.000 RK3  
=    3.000
<  Rcurr:    6.532  Rcurr-(R2+R3)/2:    1.532  MIN(Rcurr-R2,Rcurr- 
R3):    1.532
---
 > R1 = 505.000 R2 = 505.000 R3 = 505.000 R4 = 505.000 RK2 =   3.000  
RK3 =    3.000
 >  Rcurr:    6.532  Rcurr-(R2+R3)/2:  498.468  MIN(Rcurr-R2,Rcurr- 
R3):  498.468
problems for gb1_cox2
some lines from cox2.out.dif
90c89
<  NMR restraints: Bond =    3.240   Angle =     0.   Torsion =     0.
---
 >  NMR restraints: Bond =    0.   Angle =     0.   Torsion =     0.
problems for ncsu
line from abmd_ANALYSIS/mdout.dif
 >  ** NCSU-Error ** : expected list value for key 'i', got '<EMPTY>'  
instead
Can you help me to resolve these errors before I continue with further  
tests?
Best,
Philipp
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Received on Tue Mar 09 2010 - 03:00:02 PST
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