Hello Dac,
Yes I have done the same simulation with out my special
water(not using wat.off file). Here run is going. No error message
comes. But I have to take care of charges. I am telling how I have
made that off file. I made it from xleap. There is an unit "WAT". So,
going to xleap I write -
saveoff WAT wat.off
Then I get a file named wat.off in my working directory. Opening this
file I change only the charges of atoms. And everything except charges
remain unchanged.
So, why is that message coming?
Please give some hints so that I can overcome this problem.
Thanking you.
Sanjib
On 1/29/13, David A Case <case.biomaps.rutgers.edu> wrote:
> 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 Wed Jan 30 2013 - 21:00:02 PST
