CHARMM Development Project Forums User Discussion & Questions Setup, I/O, and Basic questions SOME COORDINATES NOT BUILT after ic build command

Hello all,

Some of coordinates(especially residue 2 and residue 3) are not built after ic seed and ic build command to generate a short peptide.
What could be the possible cause of this issue.


*setup for prophephe
*

! read the force field files here
open read card name "top_all36_prot.rtf" unit 25
read rtf card unit 25
close unit 25
open read card name "par_all36m_prot.prm" unit 25
read parameter card unit 25 flex
close unit 25

read sequence card
* pro-phe-phe tripeptide
*
3
PRO PHE PHE
generate A setup warn
autogenerate angles dihedrals
IC PARAM
IC SEED A 1 CA A 1 CB A 1 CG
IC BUILD
!Hbuild select all end
PRINt COOR SELEct .NOT. INITialized END

open write card name prophephesingle.pdb unit 30
write coordinates pdb unit 30
*single pro-phe-phe
*


ATOM 1 N PRO 1 -0.317 1.212 -0.746 1.00 0.00 A
ATOM 2 HN1 PRO 1 -1.085 1.688 -0.303 1.00 0.00 A
ATOM 3 HN2 PRO 1 -0.572 0.970 -1.689 1.00 0.00 A
ATOM 4 CD PRO 1 0.671 2.112 -0.847 1.00 0.00 A
ATOM 5 HD1 PRO 1 0.379 3.105 -0.436 1.00 0.00 A
ATOM 6 HD2 PRO 1 1.016 2.243 -1.898 1.00 0.00 A
ATOM 7 CA PRO 1 0.000 0.000 0.000 1.00 0.00 A
ATOM 8 HA PRO 1 9999.0009999.0009999.000 1.00 0.00 A
ATOM 9 CB PRO 1 1.458 0.000 0.000 1.00 0.00 A
ATOM 10 HB1 PRO 1 1.893 -0.468 -0.911 1.00 0.00 A
ATOM 11 HB2 PRO 1 1.893 -0.468 0.911 1.00 0.00 A
ATOM 12 CG PRO 1 1.793 1.503 0.000 1.00 0.00 A
ATOM 13 HG1 PRO 1 2.801 1.686 -0.422 1.00 0.00 A
ATOM 14 HG2 PRO 1 1.765 1.948 1.021 1.00 0.00 A
ATOM 15 C PRO 1 9999.0009999.0009999.000 1.00 0.00 A
ATOM 16 O PRO 1 9999.0009999.0009999.000 1.00 0.00 A
ATOM 17 N PHE 2 9999.0009999.0009999.000 1.00 0.00 A
ATOM 18 HN PHE 2 9999.0009999.0009999.000 1.00 0.00 A
ATOM 19 CA PHE 2 9999.0009999.0009999.000 1.00 0.00 A
ATOM 20 HA PHE 2 9999.0009999.0009999.000 1.00 0.00 A
ATOM 21 CB PHE 2 9999.0009999.0009999.000 1.00 0.00 A
ATOM 22 HB1 PHE 2 9999.0009999.0009999.000 1.00 0.00 A
ATOM 23 HB2 PHE 2 9999.0009999.0009999.000 1.00 0.00 A
ATOM 24 CG PHE 2 9999.0009999.0009999.000 1.00 0.00 A
ATOM 25 CD1 PHE 2 9999.0009999.0009999.000 1.00 0.00 A
ATOM 26 HD1 PHE 2 9999.0009999.0009999.000 1.00 0.00 A
ATOM 27 CE1 PHE 2 9999.0009999.0009999.000 1.00 0.00 A
ATOM 28 HE1 PHE 2 9999.0009999.0009999.000 1.00 0.00 A
ATOM 29 CZ PHE 2 9999.0009999.0009999.000 1.00 0.00 A
ATOM 30 HZ PHE 2 9999.0009999.0009999.000 1.00 0.00 A
ATOM 31 CD2 PHE 2 9999.0009999.0009999.000 1.00 0.00 A
ATOM 32 HD2 PHE 2 9999.0009999.0009999.000 1.00 0.00 A
ATOM 33 CE2 PHE 2 9999.0009999.0009999.000 1.00 0.00 A
ATOM 34 HE2 PHE 2 9999.0009999.0009999.000 1.00 0.00 A
ATOM 35 C PHE 2 9999.0009999.0009999.000 1.00 0.00 A
ATOM 36 O PHE 2 9999.0009999.0009999.000 1.00 0.00 A
ATOM 37 N PHE 3 9999.0009999.0009999.000 1.00 0.00 A
ATOM 38 HN PHE 3 9999.0009999.0009999.000 1.00 0.00 A
ATOM 39 CA PHE 3 9999.0009999.0009999.000 1.00 0.00 A
ATOM 40 HA PHE 3 9999.0009999.0009999.000 1.00 0.00 A
ATOM 41 CB PHE 3 9999.0009999.0009999.000 1.00 0.00 A
ATOM 42 HB1 PHE 3 9999.0009999.0009999.000 1.00 0.00 A
ATOM 43 HB2 PHE 3 9999.0009999.0009999.000 1.00 0.00 A
ATOM 44 CG PHE 3 9999.0009999.0009999.000 1.00 0.00 A
ATOM 45 CD1 PHE 3 9999.0009999.0009999.000 1.00 0.00 A
ATOM 46 HD1 PHE 3 9999.0009999.0009999.000 1.00 0.00 A
ATOM 47 CE1 PHE 3 9999.0009999.0009999.000 1.00 0.00 A
ATOM 48 HE1 PHE 3 9999.0009999.0009999.000 1.00 0.00 A
ATOM 49 CZ PHE 3 9999.0009999.0009999.000 1.00 0.00 A
ATOM 50 HZ PHE 3 9999.0009999.0009999.000 1.00 0.00 A
ATOM 51 CD2 PHE 3 9999.0009999.0009999.000 1.00 0.00 A
ATOM 52 HD2 PHE 3 9999.0009999.0009999.000 1.00 0.00 A
ATOM 53 CE2 PHE 3 9999.0009999.0009999.000 1.00 0.00 A
ATOM 54 HE2 PHE 3 9999.0009999.0009999.000 1.00 0.00 A
ATOM 55 C PHE 3 9999.0009999.0009999.000 1.00 0.00 A
ATOM 56 OT1 PHE 3 9999.0009999.0009999.000 1.00 0.00 A
ATOM 57 OT2 PHE 3 9999.0009999.0009999.000 1.00 0.00 A
TER 58 PHE 3
END

Try using seed atoms along the backbone, not a sidechain.