I am doing Drug-DNA interaction studies. For that I have selected a sequence of d(GGCCGGCCGG):d(CCGGCCGGCC). I have tried to get it from many data sources but no use. Finally, I got the structure by using "sequence to structure" software. But When I tried to feed the selected part from this whole sequence, it is showing "error in internal coordinate system". What may be the reason for this? And whenever I open this .pdb file by using chem craft, there is no problem to view all the atoms. But while trying to open it by using GaussView , it is showing "Bad atomic types are ignored" and some of the atoms are not visible. Can you please tell me why it is happening like this?
There are several formats for PDB file. If you downloaded PDB from the website for crystal structures, for instance, PDB bank. Normally, the GaussView cannot recognize it. So you should convert it into the format of GaussView can accept.
But most of the atoms from a single molecule are accepted, only some of the atoms are not accepted. Should i do any modification in that particular atom..
You can try open you pdb file in other GUI (as gabedit, that is the best) and then save (in .mol format) and re-open with gaussian view.
Is due to you are using a specific Software for construct you PDB. Sometimes the error comes for an unrecognized atom name, other times is because this particular Software with that you create the PDB does not respect the specification for PDBs, that means that each column is separated for a particular number of spaces and so on, a lot of programs are very restrictive with it.
You should check it carefully, there is not a unique solution
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