fail to guess missing coordinates

From: Liqi Feng (LIF25_at_pitt.edu)
Date: Tue May 07 2013 - 13:30:21 CDT

Hello,

I am having problem with psfgen to fill missing coordinates and generate
psf. The same procedure worked a year ago. Here is the topology file for
perchlorate:

*>>>>>> Topology File for <<<<<<<<<
*>>>>>>>>> Perchlorate anion and water<<<<<<<<<<
*
27 1

MASS 4 HT 1.00800 H ! TIPS3P WATER HYDROGEN
MASS 162 OT 15.999400 O ! TIPS3P WATER OXYGEN
MASS 164 O2L 15.999400 O ! Nucleic acid =O in phosphate or sulfate
MASS 190 CLA 35.450000 CL ! CHLORIDE Anion

AUTO ANGLE DIHE

RESI CLO4 -1.0
GROUP
ATOM CL CLA 0.580
ATOM O1 O2L -0.395
ATOM O2 O2L -0.395
ATOM O3 O2L -0.395
ATOM O4 O2L -0.395
BOND CL O1 CL O2 CL O3 CL O4
IC O1 CL O2 BLNK 1.43 111.3 0.0 0.0 0.0
IC O2 CL O1 BLNK 1.43 111.3 0.0 0.0 0.0
IC O3 CL O2 O1 1.43 111.3 120.0 34.0 2.34
IC O4 CL O2 O1 1.43 111.3 -120.0 34.0 2.34
PATCHING FIRS NONE LAST NONE

RESI TIP3 0.000 ! tip3p water model, generate using noangle
nodihedral
GROUP
ATOM OH2 OT -0.834
ATOM H1 HT 0.417
ATOM H2 HT 0.417
!BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake
BOND OH2 H1 OH2 H2
ANGLE H1 OH2 H2 ! required
ACCEPTOR OH2
PATCHING FIRS NONE LAST NONE

And psfgen file for this:
topology perchlorate.top

segment A {pdb perchl.pdb; first NONE; last NONE}

coordpdb perchl.pdb A

guesscoord

writepdb junk.pdb
writepsf junk.psf

PDB file used:
REMARK
ATOM 1 CL CLO4 1 -7.411 -2.706 2.361
ATOM 2 O1 CLO4 1 -6.248 -3.135 1.647
ATOM 4 O2 CLO4 1 -7.861 -1.422 1.910
TER
END

The thing is if I dont have O1 and O2 in my pdb file, psfgen is not able
to generate all four Os based one the internal coordinates I have in my
topology file. But in fact, I need it to do so because I dont have coor of
oxygens in another pdb file. Thank you!

Best regards,
Liqi Feng

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