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#36503 - 07/13/17 06:21 PM convert small molecule pdb file into crd file
Yonglan Liu Offline
Forum Member

Registered: 07/10/17
Posts: 13
Loc: Ohio
Dear all,
I try to convert the pdb file of a small molecule into crd file. And I use the script as follows:
bomlev -1

read rtf card name ./naga/top_all27_prot_na.rtf
read param card name ./naga/par_all27_prot_na.prm

set i 1
label pdbloop

! read pdb
read univ
* modified pdb
*
pdb
w 61 6
end

! first chain
open unit 3 read card name ./pdbfile/@i.pdb
read sequ pdb unit 3
rewind unit 3
gener O@i first none last none setup warn
read coor univ unit 3 offset 0
auto angl dihe
close unit 3

ic purge
ic param
ic fill preserve
ic build

define test sele (.not. type H*) .and. ( .not. init ) show end
coor init sele type H* end
define test sele .not. init show end

coor stat
set charge ?cgtot
energy

write psf card name ./crdfile/@i.psf
write coor card name ./crdfile/@i.crd

delete atom sele all end

incr i by 1
if i .lt. 16.5 goto pdbloop

stop

But error occurs as follows:
CHARMM> ic purge

CHARMM> ic param

CHARMM> ic fill preserve

***** LEVEL 1 WARNING FROM *****
***** FILLIC called with a null IC table
******************************************
BOMLEV ( -1) IS NOT REACHED. WRNLEV IS 5


CHARMM> ic build

***** LEVEL 1 WARNING FROM *****
***** BILDC called with a null IC table
******************************************
BOMLEV ( -1) IS NOT REACHED. WRNLEV IS 5


**** WARNING **** FOR THIS OPERATION, THERE WERE 8 MISSING COORDINATES

NBONDA>> Maximum group spatial extent (12A) exceeded.
Size is 10007.62 Angstroms and starts with atom: 1
Please check group boundary definitions.
WARNING: ATOMS O1 1 NAA H2 AND O1 1 NAA H5 ONLY 0.00 A. APART

***** LEVEL -2 WARNING FROM *****
***** Some atoms have undefined positions
******************************************
BOMLEV ( -1) IS REACHED - TERMINATING. WRNLEV IS 5



/---------\
/ \
/ \
/ \
! XXXX XXXX !
! XXXX XXXX !
! XXX XXX !
! X !
--\ XXX /--
! ! XXX ! !
! ! ! !
! I I I I I !
! I I I I !
\ /
-- --
\---/
XXX XXX
XXXX XXXX
XXXXX XXXXX
XXX XXX
XXX XXX

My pdb file is:
CRYST1 60.782 56.958 56.303 90.00 90.00 90.00 P 1 1
ATOM 1 C1 NAA O 1 -2.624 -4.409 2.631 1.00 0.00 O1
ATOM 2 H2 NAA O 2 -2.018 -3.876 1.926 1.00 0.00 O1
ATOM 3 H3 NAA O 3 -2.277 -4.554 3.632 1.00 0.00 O1
ATOM 4 C4 NAA O 4 -3.829 -4.899 2.252 1.00 0.00 O1
ATOM 5 H5 NAA O 5 -4.435 -5.431 2.955 1.00 0.00 O1
ATOM 6 C6 NAA O 6 -4.327 -4.690 0.810 1.00 0.00 O1
ATOM 7 O7 NAA O 7 -3.615 -4.064 -0.017 1.00 0.00 O1
ATOM 8 N8 NAA O 8 -5.635 -5.221 0.400 1.00 0.00 O1
ATOM 9 H9 NAA O 9 -5.522 -6.151 0.047 1.00 0.00 O1
ATOM 10 C10 NAA O 10 -6.204 -4.366 -0.651 1.00 0.00 O1
ATOM 11 H11 NAA O 11 -6.326 -3.372 -0.275 1.00 0.00 O1
ATOM 12 H12 NAA O 12 -5.545 -4.350 -1.494 1.00 0.00 O1
ATOM 13 C13 NAA O 13 -7.574 -4.923 -1.081 1.00 0.00 O1
ATOM 14 N14 NAA O 14 -8.618 -4.011 -1.568 1.00 0.00 O1
ATOM 15 H15 NAA O 15 -9.200 -4.490 -2.226 1.00 0.00 O1
ATOM 16 H16 NAA O 16 -9.174 -3.699 -0.798 1.00 0.00 O1
ATOM 17 O17 NAA O 17 -7.799 -6.160 -1.014 1.00 0.00 O1
END

Please give me advice to fixed it
_________________________
Yonglan Liu
University of Akron

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#36504 - 07/14/17 11:49 AM Re: convert small molecule pdb file into crd file [Re: Yonglan Liu]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8079
Loc: 39 03 48 N, 77 06 54 W
That script was designed for a protein import, where most of the heavy atoms have coordinates, and won't work for a drug molecule with all coordinates unknown.

Check the topology file for the NAA residue to see if there is an IC table defined for that residue; if so, one can use commands like

IC PARAM
IC SEED atom atom atom
IC BUILD

If there is no IC table, you must provide one, either manually by editing the topology file, or via the IC GENERATE command (see intcor.doc). While the latter may be easier, it is known to have some issues, esp. with ring systems.
_________________________
Rick Venable
computational chemist


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