grompp error : atom name in topol.top and solv.gro does not match
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Entering edit mode
7.5 years ago

hello,

I am using gromacs to energy minimize Protein-Ligand complex. I have performed all the steps as described in tutorial but i am getting this error while running grompp :

Warning: atom name 24913 in topol.top and solv.gro does not match (CBI - OW)
Warning: atom name 24914 in topol.top and solv.gro does not match (CBH - HW1)
Warning: atom name 24915 in topol.top and solv.gro does not match (CBG - HW2)
Warning: atom name 24916 in topol.top and solv.gro does not match (CBF - OW)
Warning: atom name 24917 in topol.top and solv.gro does not match (CBE - HW1)
Warning: atom name 24918 in topol.top and solv.gro does not match (CBD - HW2)
Warning: atom name 24919 in topol.top and solv.gro does not match (CBA - OW)
Warning: atom name 24920 in topol.top and solv.gro does not match (CAX - HW1)
Warning: atom name 24921 in topol.top and solv.gro does not match (CAV - HW2)
Warning: atom name 24922 in topol.top and solv.gro does not match (CAS - OW)
Warning: atom name 24923 in topol.top and solv.gro does not match (CAP - HW1)
Warning: atom name 24924 in topol.top and solv.gro does not match (CAM - HW2)
Warning: atom name 24925 in topol.top and solv.gro does not match (O1 - OW)
Warning: atom name 24926 in topol.top and solv.gro does not match (C1 - HW1)
Warning: atom name 24927 in topol.top and solv.gro does not match (C2 - HW2)
Warning: atom name 24928 in topol.top and solv.gro does not match (O2 - OW)
Warning: atom name 24929 in topol.top and solv.gro does not match (H22 - HW1)
Warning: atom name 24930 in topol.top and solv.gro does not match (C3 - HW2)
Warning: atom name 24931 in topol.top and solv.gro does not match (O3 - OW)
Warning: atom name 24932 in topol.top and solv.gro does not match (H32 - HW1)
(more than 20 non-matching atom names)

WARNING 1 [file topol.top, line 50]:
  42 non-matching atom names
  atom names from topol.top will be used
  atom names from solv.gro will be ignored


Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:  2583    Protein residues
There are:     1      Other residues
There are: 115662      Water residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group rest is 768831.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 144x144x144, spacing 0.109 0.109 0.109
Estimate for the relative computational load of the PME mesh part: 0.23
This run will generate roughly 29 Mb of data

There were 2 notes

There was 1 warning

-------------------------------------------------------
Program grompp, VERSION 4.6.5
Source code file: /build/buildd/gromacs-4.6.5/src/kernel/grompp.c, line: 1910

Fatal error:
Too many warnings (1), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

please, can anyone help me with this error.

gromacs software-error • 6.5k views
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Entering edit mode
4.9 years ago

you need to make sure that what you have written in the top file corresponds your pdb file

For example if in your pdb file, the protein is first written and next the ligand is written make sure you have the same order in your top file

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