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Hbuild command changes original oxygen coordinates
#37821 03/27/20 07:19 AM
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Hello,

I am trying to use Hbuild command to add hydrogen atoms to water molecules. The program finished normally, but I found that most of the oxygen coordinates are changed.
FOr instance, in the original pdb:
ATOM 4 OH2 TIP3 2 -0.058 3.502 5.369 1.00 0.79
But once I used Hbuild command, it becomes
ATOM 4 OH2 TIP3 2 0.058 3.502 5.369 1.00 0.79 W
ATOM 5 H1 TIP3 2 0.086 3.399 6.320 1.00 0.00 W
ATOM 6 H2 TIP3 2 0.293 2.639 5.028 1.00 0.00 W

Why did this happen?
If I guess correctly,charmm uses one of oxygen coor as a reference to build a cut-off and all atom coor outside this cut-off are modified. How could I turn that off?

Last edited by Allen_123; 03/27/20 08:47 AM.
Re: Hbuild command changes original oxygen coordinates
Allen_123 #37822 03/27/20 01:57 PM
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Strange. This should not happen. Please post your input file - a brief but complete file showing the suspect behavior, but with no other stuff.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Hbuild command changes original oxygen coordinates
Allen_123 #37823 03/28/20 11:23 PM
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I seem to recall that COOR SHAKE would perturb heavy atom coordinates. My workaround was

CONS FIX SELE .NOT. HYDROGEN END
COOR SHAKE
CONS FIX SELE NONE END


Rick Venable
computational chemist


Moderated by  John Legato, lennart 

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