WARNING: Problem detected in: SIDE MOLE FILES

[meghaparashar2]

Dear @hernanchavezthielemann

While generating lammps files for one of my system I am getting one error and warning.
""""
Loading side molecule files:
Warning!! -- Problem detected in :
SIDE MOLE FILES
""""

Here are the files:
bon2itp.txt
forcefielditp.txt
mchitp.txt
nbitp.txt
topologytop.txt

I am not able to figure it out. Can you please take a look and suggest a solution.

Thanks,
Megha

[hernanchavezthielemann]

Hi Megha, @meghaparashar2

I am missing your coords file, the ".gro".

best,
Hernan

[meghaparashar2]

Dear @hernanchavezthielemann
I apologize for this.
Here's the coordinate file:
coor.txt

[hernanchavezthielemann]

Hi @meghaparashar2,

I just checked it, and seems like there are may mismatches in your files causing the problems.

In the gro file I found that the third column is wrongly indented.
Following C formatting, the right format is :
%5d%-5s%5s%5d%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f

Then your molecules index first column, have 1 for BTA and 1 for MCH, I am not sure if this is a right thing to do, so I would not modify GRO2LAM to accept that.

Then there is a mismatch between your atom types in bonded interactions and the ones declared under [ atoms ] directive. I think there is a confusion between atom type and atom tag

Example;

[ atoms ]
; nr type resi res atom cgnr charge mass ; qtot bond_type
1 ca 1 BTA C1 1 -0.137600 12.01000 ; qtot -0.138
2 ca 1 BTA C2 2 -0.032600 12.01000 ; qtot -0.170
3 ca 1 BTA C3 3 -0.137600 12.01000 ; qtot -0.308
...

[ bondtypes ]
; ai aj funct r k
C1 C2 1 1.3980e-01 3.1681e+05 ; C1 - C2
C1 C6 1 1.3980e-01 3.1681e+05 ; C1 - C6
...

bond type should be just:
ca ca 1 1.3980e-01 3.1681e+05 ;

Please take a look and try to fix your files, then let me know if you still need some help.

best,
Hernan.

[meghaparashar2]

Dear @hernanchavezthielemann

Thanks for your inputs.
I am able to resolve this issue.

There's one more thing.
When I am having one residue (solute) and many solvent molecules I am able to get a perfect data file.
But if I am having only solute in a box with more than one molecules, in the data file I am getting all values for one residue. Though in the topology file nmols are mentioned to be more than one.
Same is happening when I am having a box full of solvent molecules. In the generated data file only parameters corresponding to one molecule is written.

Here are the files for first case (solute):
allovertop.txt
bon3itp.txt
dimergro.txt
forcefielditp.txt
nbitp.txt

Thanks,
Megha

[hernanchavezthielemann]

Hi @meghaparashar2,
I will try to look at it later today,
But considering what you have said, it seems like it is being read one time, because it is in your main top file.
I would try to make a new itp file with the molecule definition, and include it from the top file.
I will be back later,
Cheers,
Hernan.

[hernanchavezthielemann]

Hello @meghaparashar2,

Indeed, that's is a good issue that I have had for some time.
The solution I think is actually easy to implement, but I need time for that, and then test.

Probably, since there is a work around, I do not think of it as something critical.
Attached you can find the files to make it work as mentioned in my previous message.

Best,
Hernan.
megha2.zip