[gmx-users] Re: Re: Fw: Re: Polymer-protein problem

[P.R.Anand Narayanan]

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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