Plumed serial of an atom cannot be zero error

[Herodion Hartono]

Hi all,

I encountered this error while trying Plumed2.8:

+++ PLUMED error
+++ at AtomNumber.h:95, function PLMD::AtomNumber&
PLMD::AtomNumber::setSerial(unsigned int)
+++ assertion failed: i>0
+++ message follows +++
serial of an atom cannot be zero

While I checked that the atoms do exist in the pdb file

This is the .dat :

# Activate MOLINFO functionalities
MOLINFO STRUCTURE=step6.6_equilibration.pdb
# you should use MOLINFO shortcuts
d1: DISTANCE ATOMS=1711,3917
#Distance metadynamics
metad: METAD ARG=d1 SIGMA=0.1 HEIGHT=0.1 PACE=200 BIASFACTOR=4 FILE=HILLS_TM3-6 GRID_MIN=0.7 GRID_MAX=1.9
# Print both collective variables on COLVAR file every 10 steps
PRINT ARG=d1 FILE=COLVAR_TM3-6 STRIDE=10

From .pdb file;

ATOM   1711  CA  ARG   129      54.370  64.760  84.650  1.00  0.00  

ATOM   3917  CA  VAL   269      59.480  72.090  83.640  1.00  0.00

 

Cannot post whole .pdb because file is too big.

I wonder what I did wrong?

Thank you in advance, Odi

[Michele Invernizzi]

Dear  Odi,

What do the first few lines of the pdb look like? Is there an atom numbered as 0, or a line that might be misinterpreted as an atom with index zero?

Also, in this specific plumed input you do not really need the MOLINFO line, you can delete it and everything should be fine. MOLINFO is useful if you want to refer to atoms without explicitly using their index, see https://www.plumed.org/doc-v2.8/user-doc/html/_m_o_l_i_n_f_o.html

Hope this helps!

Best,

Michele

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[Herodion Hartono]

Hi Michele,

Initial lines of the .pdb files are as follows:

TITLE     Title
REMARK    THIS IS A SIMULATION BOX
CRYST1  126.869  126.869  126.869  90.00  90.00  90.00 P 1           1
MODEL        1
ATOM      1  N   THR    21      72.580  73.890  43.420  1.00  0.00            
ATOM      2  HT1 THR    21      72.780  72.870  43.410  1.00  0.00            
ATOM      3  HT2 THR    21      72.840  74.260  42.490  1.00  0.00            
ATOM      4  HT3 THR    21      71.610  74.110  43.720  1.00  0.00            
ATOM      5  CA  THR    21      73.400  74.540  44.580  1.00  0.00            
ATOM      6  HA  THR    21      73.100  75.570  44.700  1.00  0.00            
ATOM      7  CB  THR    21      73.230  73.790  45.880  1.00  0.00            
ATOM      8  HB  THR    21      73.800  74.250  46.720  1.00  0.00            
ATOM      9  OG1 THR    21      73.410  72.390  45.750  1.00  0.00            
ATOM     10  HG1 THR    21      73.020  71.910  46.490  1.00  0.00            
ATOM     11  CG2 THR    21      71.750  73.760  46.280  1.00  0.00            
ATOM     12 HG21 THR    21      71.420  74.800  46.490  1.00  0.00            
ATOM     13 HG22 THR    21      71.650  73.130  47.190  1.00  0.00            
ATOM     14 HG23 THR    21      71.040  73.400  45.500  1.00  0.00            
ATOM     15  C   THR    21      74.860  74.710  44.300  1.00  0.00            
ATOM     16  O   THR    21      75.440  74.030  43.420  1.00  0.00

It's a product of gmx editconf from a .gro file to a .pdb file. First atom is numbered 1.

Commenting out the MOLINFO line on the .dat file works! Thanks a lot!

Cheers, Odi

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