Pd Nanoparticle

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1

GROMACS version:2020.4
GROMACS modification: No
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I am working on a MD simulation of a Pd nanoparticle and I have run into a problem with gmx pdb2gmx step. I start from a pdb generated using Materials Studio which contains the coordinates of 1833 Pd atoms, and I have updated the opls-aa force-field by adding the missing atomtype to atomtypes.atp, new aminoacid to aminoacid.trp , and nonbonded interactions in ffnonbonded.itp.

I run
gmx pdb2gmx -f np.pdb -o test.gro -ff opls
and it generates the test.gro file without errors, but it only contains 1 atom in it instead of the 1833 I have started with. What do I need to do in order to generate the proper Pd nanoparticle in the configuration that I start with in the .pdb file ?

Many thanks,
Lena

2

Hi Lena,

This sounds strange - could you share your data somewhere, so I can have a look into what is happening? It might have to do with the np.pdb

3

Does your .rtp entry only specify a single atom, e.g. this is a purely nonbonded model? If it is, then you’ll only get a [moleculetype] with a single atom but then there will be 1833 of them listed under [molecules].

4

Thanks so much for a prompt response! I found the issue, it was a minor thing: all residues had the same number in my pdb for some mysterious reason. We don’t know how it happened, but once fixed the simulation ran perfectly well. Thanks again!

5

Hi! Currently I am facing a similar problem where my system (a copper surface) was built in Materials Studio. Checking the pdb file at the residuename it says “MOL”. ¿Could you please explain me how did you add, in your case the Pd nanoparticle to the aminoacid.rtp file and what was his name in the pdb file you obtained from Materials Studio?