I am trying to build the PDB and PSF files for monomer of polyethylene glycol (PEGM). However, one hydrogen atom connected to each carbon and oxygens overlaps with another bond. I have attached the snip of the pdb generated below. Please help me to rectify this error.
Script:
* make a PDB and PSF files fo PEGM *
read rtf card name top_all35_ethers-oh.rtf read param card name par_all35_ethers-oh.prm
read sequ PEGM 1
generate PEGM { first GCL0 last GCL3 } a setup
ic generate ic param ic seed PEGM 1 C1 PEGM 1 O1 PEGM 1 C2 ic build
hbuild coor orient
write coor pdb name peg1.pdb * PDB file of custom sequence. * write psf card xplor name peg1.psf * PSF *
Possibly conflicting internal coordinates from using both the SETUP keyword of GENERATE, and using IC GENERATE; try omitting each separately, starting with IC GENERATE.