From: faride badalkhani (farideh.khamseh_at_gmail.com)
Date: Tue Apr 26 2016 - 16:22:02 CDT
It is an internal alkyne carbon!
On Wed, Apr 27, 2016 at 1:47 AM, faride badalkhani <
> Thanks for your answer and time.
> On Tue, Apr 26, 2016 at 7:44 PM, Arash Azari <arashazari.temp_at_gmail.com>
>> salam Farideh,
>> I am not expert in this field, but I think this question has been
>> answered in the mailing-list.
>> Based on my previous experience, it simply indicates that the system did
>> not well minimized before running the simulation. You need much longer
>> As I remember from your previous emails, you used 0.5 fs time step which
>> is not the step which normally people use in their MD simulations; you
>> should use something around 2 fs. Please have a look at user manual.
>> Please repeat everything with this time step and minimize the system much
>> longer; it depends on the size of your system and the number of atoms.
>> You should perform: minimization, (gradual heating depending on what you
>> have done and need) equilibration, and main simulation. In some cases it is
>> recommended to minimize the system a couple of times followed by
>> I hope this helps.
>> One more thing; please do not post too much question to the mailing list
>> as people will ignore very frequent questions.
>> Probably you can get much better help from your colleagues at your
>> research group (Department).
>> Please let me know if you solve the problem.
>> Good luck!
>> Best regards,
>> On Mon, Apr 25, 2016 at 5:42 PM, faride badalkhani <
>> farideh.khamseh_at_gmail.com> wrote:
>>> Dear NAMD users,
>>> I am trying to simulate a hyperbranched polymer in a water box. I
>>> defined the patches and built the Protein Structure File (PSF) using a tcl
>>> command, and there was nothing strange in psf file format. when I run a NVT
>>> simulation for 500 ps I got this error message:
>>> ERROR: Constraint failure in RATTLE algorithm for atom 6!
>>> ERROR: Constraint failure; simulation has become unstable.
>>> ERROR: Exiting prematurely; see error messages above.
>>> So, I reviewed NAMD mailing list and checked periodic cell size. I had
>>> minimized the system for 25 ps. I tried looking at my psf and pdb files in
>>> VMD. There was no atom with (0, 0, 0) coordinates.
>>> I set the MARGIN parameter to 5 in the NAMD configuration file.
>>> But I got the same error. Therefore, I tried the simulated annealing in
>>> vacuum. But, it does not work, too.
>>> Atom 6 (in fact, 5) is an internal alkyne carbon! and the residue has a
>>> shape of
>>> RESI POC -0.235 !
>>> ATOM HA H 0.421
>>> ATOM O1 OH1 -0.899 !
>>> ATOM C1 CT2 0.198 ! H1
>>> ATOM H1 HA2 0.090 ! __ |
>>> ATOM H2 HA2 0.090 ! H3--C3==C2--C1--O1--HA
>>> ATOM C2 CGT1 -0.015 ! |
>>> ATOM C3 CGT2 -0.410 ! H2
>>> ATOM H3 HGP 0.290 !
>>> BOND H3 C3 C3 C2 C2 C1 C1 O1
>>> BOND C1 H1 C1 H2 O1 HA
>>> DONOR O1 HA
>>> ACCEPTOR O1
>>> PATCHING FIRS NONE LAST NONE
>>> Any help will be appreciated.
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