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Carbon and oxygen atoms occupy same place in crd file
#36910 03/20/18 04:58 PM
Joined: Mar 2018
Posts: 2
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umesh Offline OP
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Joined: Mar 2018
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Hello all,

I want to create a .crd file from my pdb file and want to use ACE and CT3 patch.

My charmm script is as follow:
.......................................................................
*CHARMM Tutorial
*

open read unit 11 card name top_all36_prot.rtf
read rtf card flex unit 11
close unit 11
open read unit 12 card name par_all36_prot.prm
read para card flex unit 12
close unit 12

open read unit 13 card name input_b.pdb
read sequ pdb unit 13
gene b setu first ACE last CT3 warn

REWInd UNIT 13
READ COOR PDB UNIT 13
CLOSE UNIT 13

!Involves known atomic coordinates and fills in missing coordinates
IC FILL
!Will retrieve standard coordinates from the parameter file

IC PARAmeters

PRINt COOR

!Will find the Cartesian coordinates previously unknown
IC BUILd

IC GENErate

!Rebuild all hydrogen coordinates
HBUILD SELEct HYDRogen END

!Check for remaining missing atoms
PRINt COOR SELEct .NOT. INITialized END

open write unit 14 card name "test.crd
write coordinates card unit 14
close unit 14
stop


...................................................

I got test.crd file and I was looking good.
But when I checked my .crd in pymol to see the patch, I found something is wrong. I observed Carbon and oxygen atom merged together. Please check .crd file i have attached.

Please help me, what is wrong in my script?

Thanks,
Umesh

Attached Files
test.zip (18.46 KB, 93 downloads)
Re: Carbon and oxygen atoms occupy same place in crd file
umesh #36911 03/20/18 05:41 PM
Joined: Sep 2003
Posts: 8,507
rmv Online Content
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Online Content
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Joined: Sep 2003
Posts: 8,507
When viewing CHARMM files, using the PSF to define the bonding is recommended; if PyMol doesn't do that, use VMD.

There is no need for IC GENErate in this script. (In most cases, I've found it's best to not use IC GENErate at all.)

Please be specific about which C and O atoms are overlapped.


Rick Venable
computational chemist


Moderated by  lennart, rmv 

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