CHARMM Development Project Forums User Discussion & Questions Setup, I/O, and Basic questions Error in structure after building pdb using ic build.

Hi,

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
*

stop


PDB generated:

ATOM 1 C0 PEGM 1 -2.661 0.246 -0.241 1.00 0.00 PEGM
ATOM 2 H0A PEGM 1 -3.472 0.894 0.153 1.00 0.00 PEGM
ATOM 3 H0B PEGM 1 -2.833 -0.795 0.106 1.00 0.00 PEGM
ATOM 4 OG0 PEGM 1 -2.881 -1.085 0.203 1.00 0.00 PEGM
ATOM 5 HG0 PEGM 1 -3.743 -1.338 -0.137 1.00 0.00 PEGM
ATOM 6 C1 PEGM 1 -1.302 0.746 0.253 1.00 0.00 PEGM
ATOM 7 H1B PEGM 1 -0.490 0.098 -0.140 1.00 0.00 PEGM
ATOM 8 H1A PEGM 1 -1.129 1.787 -0.094 1.00 0.00 PEGM
ATOM 9 O1 PEGM 1 -0.245 -0.060 -0.231 1.00 0.00 PEGM
ATOM 10 C2 PEGM 1 0.991 0.435 0.248 1.00 0.00 PEGM
ATOM 11 H2A PEGM 1 1.134 1.479 -0.104 1.00 0.00 PEGM
ATOM 12 H2B PEGM 1 1.819 -0.200 -0.135 1.00 0.00 PEGM
ATOM 13 C3 PEGM 1 2.165 -0.408 -0.253 1.00 0.00 PEGM
ATOM 14 H3A PEGM 1 2.056 -1.458 0.094 1.00 0.00 PEGM
ATOM 15 H3B PEGM 1 3.122 0.000 0.136 1.00 0.00 PEGM
ATOM 16 OG3 PEGM 1 3.389 0.114 0.244 1.00 0.00 PEGM
ATOM 17 HG3 PEGM 1 4.080 -0.455 -0.103 1.00 0.00 PEGM
TER 18 PEGM 1
END

Possibly conflicting internal coordinates from using both the SETUP keyword of GENERATE, and using IC GENERATE; try omitting each separately, starting with IC GENERATE.