Dear Sir,
I energy optimised the polymer-protein structure using HYPERCHEM. The moment I
created peptide bonds between them, the pdb was saved like the format mentioned
previously. for eg;
HETATM 1 N 1 -24.998 12.703 12.925
>
> HETATM 2 C 2 -24.749 12.813 11.460
>
> HETATM 3 C 3 -24.428 11.438 10.881
>
> HETATM 4 O 4 -25.267 10.544 11.131
>
> HETATM 5 H 5 -25.225 13.528 13.462
>
> HETATM 6 H 6 -25.636 13.216 10.970
>
> HETATM 7 H 7 -23.903 13.478 11.291
So, if there is NO other way of using this type of pdb file in GROMACS; can you
please suggest any other software where I can successfully make covalent bonds
between the protein and polymer, optimise them under force-field algorithms and
THEN use the pdb file in GROMACS?
Eagerly awaiting your advise and reply!!!
>>>"What program did you use to create this new PDB file? It looks like it
>>>severely
crippled the file, changing just about everything about it. There is certainly
no way to use this .pdb file, since there aren't even any residue names defined
in it.
-Justin"
<<<<
Thanking you,
Regards,
Anand
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