I have been working with a complex system that involves 5 different atoms and 3 different molecules. However 2 of the atoms are present in 2 different molecules i.e O & H. Now when I am creating my structure (via Material studio) in .pdb, .car or .mol2 format I can see that these files acknowledge the different O &H atoms used in the molecules but when I am converting them into data file for lammps using openbable these information gets lost. What I get instead is same atom type for all the O & H. Can anyone suggest a way to work around it?
You have multiple options:
1. Define the atoms in Materials Studio somthing different than O and H (e.g. to S and P), convert the MS to Lmp data and then in the data file updates the parameters of S and P to that of O and H.
2. In materials studion you can define different types of O, H, C, ... by assigning cvff forcefile parametrs. Then use msi2lmp convertor with cvff and you have multiple O, H, C, in the lammps data file.
You need to create solutions and come up with the best options based on the type of atoms you have in the system.
Dr. Asiaee,
Thank you for your suggestions. The 1st one works for me! for the second one; I have tried it before but I have some atoms in my structure which are not recognized by the cvff ff.
I really appreciate your help. Stay safe.
Cheers,
Nirmalay.
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