Sorry, forgot to post which system I am using:
amber10 and ambertools1.2 with each with bugfixes from yesterday,
compiled with -static gfortran (gcc 4.1.2), serial version on Intel
Xeon with CentOS 5.3, x86-64
Best,
Philipp
On Mar 9, 2010, at 11:45 AM, Philipp Marquetand wrote:
> 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 - 03:00:03 PST
