On Tue, Jan 29, 2013, Sanjib Paul wrote:
> I am going to do a simulation of human carbonic
> anhydrase II using 2CBA.pdb. As it lacks of two N-terminal
> residues(NMET and SER) I attached them with the help of SWISS PDB
> VIEWER. Here some unwanted bond is formed between NMET and crystal
> waters.
This is not clear: what makes you think there is a bond between the protein
and a water molecule. You need to tell us *exactly* what you did, and what
result makes you think there is such a bond.
I thought after minimization those bonds will be removed and I
> would get a good structure. But in pmemd.cuda those bonds are not
> removing. Then I tried it in sander. Here those bonds are removing
> very soon.
Bonds never appear or disappear during minimzation or MD. As a guess,
you may be deducing the presence or absence of a bond from some graphics
program, but without details, people on the list can't be of much help.
> When I prepared the
> system I used a '.off' file for the water bonded to Zn ion as the
> charges of atoms of this water molecule would be different from other
> water molecules. I am attaching this file here. Please help me. If
> anyone has any other query please let me know.
>
I suggest you work in smaller steps. Try to get everything running
without worrying about the charges on some "special" water molecule, (i.e.
don't use your water .off file, but treat zinc-bound water as a ordinary
water molecule.) That will also indicate whether the error messages are
related to the special water you are using. Once you have that working,
you can re-examine exactly what you are doing with the zinc-bound water.
...dac
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Received on Tue Jan 29 2013 - 07:30:04 PST
