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#34392 - 09/13/14 11:17 PM Creating IC table from coordinates
chamila Offline
Forum Member

Registered: 02/19/14
Posts: 19
Hi,

I have added a new residue to RTF file and I need to add IC table to this residue. (my next step is to do a constrained optimization to this residue so need to constrain the internal coordinates)

I change the 'complex PDB input examples' script according to my residue as below,

* energy minimization of 24-3-4-afructose
*
read rtf card name top_all36_boron_sugar-new.rtf
read para card name par_all36_boron_sugar-p9.prm

open unit 10 read card name 24d-30.pdb
read sequ pdb unit 10
rewind unit 10
gener BAF3 setup warn
read coor pdb unit 10
Close unit 10

! SAVE THE COMPLETED PSF
open unit 1 write card name 24d-30.psf
write psf card unit 1
* the psf of 24d-30
*

close unit 1

open unit 1 write card name 24d-30.crd
write coor card unit 1
*INITIAL CHARMM coords
*

ic purge
ic param
ic fill preserve
ic build
print ic

!open unit 1 write card name IC-BUILT.ic
!write ic card unit 1
!* CHARM IC Table for IC-BUILT
!*

stop


The output has errors like,

CHARMM>

CHARMM> ic purge

CHARMM> ic param

CHARMM> ic fill preserve

***** LEVEL 1 WARNING FROM *****
***** FILLIC called with a null IC table
******************************************
BOMLEV ( 0) IS NOT REACHED. WRNLEV IS 5


CHARMM> ic build

***** LEVEL 1 WARNING FROM *****
***** BILDC called with a null IC table
******************************************
BOMLEV ( 0) IS NOT REACHED. WRNLEV IS 5

I have used the same pdb file in an energy minimization calculation and it worked fine. Here I do not understand why the IC FILL command doesn't read the cartesian coordinated from the pdb file. Could you please tell me what I did wrong.

Thank you.

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#34394 - 09/15/14 12:39 PM Re: Creating IC table from coordinates [Re: chamila]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8373
Loc: 39 03 48 N, 77 06 54 W
The error message is a huge hint here; the problem arises because, as the message implies, there is no IC table. The SETUP keyword expects entries and data for an IC table to be included in the RESIdue definition in the topology. The error suggests that you did not include IC table data in your residue description.

I strongly suggest that you create the IC table by hand; as a first pass, you can focus on heavy atoms and use HBUILD to place the H atoms (no IC entries needed).

It is possible to use IC GENERATE to do so, but that is an imperfect tool and may not give optimal results. Caveat emptor.
_________________________
Rick Venable
computational chemist


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