I have to downloaded sdf file of Benzene from RCSB.org . I have to convert it into pdb file . I have tried AVOGADRO and Open Babel . After conversion I get .pdb file. But in that file building blocks are missing . Only LIG is written instead of building blocks. I have to use it in GROMACS .Seeing a software or a method.
I need pdb file of decane-1-thiole also.I want to make silver nanoparticle capping by decane -1-thiole. I have to use it on gromacs
You have used Avogadro which itself is a molecule drawing software. All different kind of building blocks are in there inbuilt in Avogadro.
And only for peptide different amino acids are labelled in the PDB file but for any other kind of ligand you will see LIG/UNK etc. as residue name.
I am using silver atom(decane thiol silvernanoparticle) silver is not defined in the topology..that is my problem...
I think you should take a look to gromacs topology and parameter files. If these libraries do not contain your molecules parameters you should build new parameters for it. First you have to define charges after optimization of molecule. And there is too many literature and tutorials on web.
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