[gmx-users] co-ordinate number mismatch

Christopher Neale chris.neale at mail.utoronto.ca
Sat Oct 13 05:02:28 CEST 2012

grep out each molecule type and pipe it to wc -l to find out how many atoms of each type you have in your .gro 
file, then compare this value to your .top file. This will help you identify which molecule is incorrectly represented
in the .top file.


# find number of SOL in the .gro
grep SOL my.gro |wc -l

# find number of SOL in the .top
grep ^SOL my.top |awk '{s+=$2}END{print s}'


-- original message --

I am trying to simulate a proein-ligand simulation. My protein is a
tetramer and has 3 ligands, ATP, OXL and FDP. As I am using
amber99sb-ildn forcefield, I generated the topology and co-ordiante
files fusing Acpype. I have appended the information to cinluded in
the topology file i.e. complex.top and also the atomtypes information
in tandem to the acpype instructions. Also, I appended the
co-ordinates of the ligands into my file generated after pdb2gmx step
where the topology of protein was generated. However, after defining
my box, when I preprocess my system before adding ions, I come across
the final error.

Fatal error:
number of coordinates in coordinate file (system_solv.gro, 315767)
             does not match topology (complex.top, 315771)

I do understand that somewhere either the information is not updated,
which I have seen several times to be getting updated or else there is
a problem with SOL molecules. I have tried running a simulation of
another protein-ligand system in exactly the same manner and didn't
encounter any problem. It would be really helpful if someone possibly
give me the suggestion and possible solution. I have appended partial
contents  of both the files below:

complex.top file contents:

[ molecules ]
; Compound        #mols
Protein_chain_A     1
Ion_chain_A2        1
Other_chain_A3      1
Ion_chain_A4        1
Protein_chain_B     1
Ion_chain_B2        1
Other_chain_B3      1
Ion_chain_B4        1
Protein_chain_C     1
Ion_chain_C2        1
Other_chain_C3      1
Ion_chain_C4        1
Protein_chain_D     1
Ion_chain_D2        1
Other_chain_D3      1
Ion_chain_D4        1
SOL                 1
SOL                 1
SOL               165
SOL                 1
SOL                 1
SOL               377
SOL                 1
SOL                 1
SOL               303
SOL                 1
SOL                 1
SOL               398
FDP_A               1
FDP_B               1
FDP_C               1
FDP_D               1
ATP1                1
ATP2                1
ATP3                1
ATP4                1
OA_m                1
OB_m                1
OC_m                1
OD_m                1
SOL             92850

contents from system_solv.gro:

92849SOL    HW215761  15.757  16.224  11.514
92850SOL     OW15762  16.249  14.948  11.340
92850SOL    HW115763  16.284  14.907  11.256
92850SOL    HW215764  16.159  14.910  11.360
92851SOL     OW15765  14.935  15.974  11.472
92851SOL    HW115766  15.034  15.963  11.463
92851SOL    HW215767  14.895  15.888  11.504
  16.39712  16.39712  11.59451   0.00000   0.00000   0.00000   0.00000
  8.19856   8.19856

Ankita Naithani

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