From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Aug 09 2010 - 05:07:39 CDT
dear joyce,
On Mon, Aug 9, 2010 at 5:29 AM, Kwee Hong <joyssstan0202_at_gmail.com> wrote:
[,,,,]
> 4 cadmium ions are actually tetrahedrally bound to my protein. So, I've
> added the below portion into the parameter file to define the bond between
> the sulphur from cystein and the cadmium ion:
>
> SS CD 0.0000 2.4670
>
> The bond lenth was taken from my literature review. I leave the force
> constant value at 0.000 as I do not find any such value in my literature
if you leave a force constant at zero,
that is the same as not defining a force at all.
> review. I'm afraid that the warning might be referring to this bond length.
> If so, what would be its effect to my simulation and does that mean that I
> would need to make a guess on that value?
there is no need to guess. each force field has
a well laid out set of rules as to how its parameters
are defined. typically, force constants for bonds
can be inferred from quantum chemical vibrational
analysis calculations. in the case of multi-valent
metal ions, however, i would not expect too much
accuracy, since their interactions are notoriously
contain many-body contributions, that typical
biomolecular forcefield only consider in an average
way (as they are not as prevalent in bonds between
C, N, O, H, ...).
cheers,
axel.
> Thanks.
>
> Regards,
> Joyce
>
>
>
>
> On Mon, Aug 9, 2010 at 4:13 PM, Bjoern Olausson <namdlist_at_googlemail.com>
> wrote:
>>
>> On Monday 09 August 2010 09:28:16 you wrote:
>> > Hi everyone,
>> >
>> > I'm new to NAMD. While I energy minimized my system, I got a warning as
>> > below in the log file:
>> >
>> > Warning: Ignored 12 bonds with zero force constants.
>> >
>> > Can anyone tell me what does that mean and how it may affect my
>> > simulation?
>> >
>> > Thanks.
>> >
>> > Regards,
>> > Joyce
>>
>> Hi,
>>
>> I guess you are using the TIP3 Water model with SHAKE and probably have 12
>> Water molecules in your system?
>>
>> If this is correct, you don't have to worry about the Warning.
>>
>> Cheers
>> Bjoern
>>
>> --
>> Bjoern Olausson
>> Martin-Luther-Universität Halle-Wittenberg
>> Fachbereich Biochemie/Biotechnologie
>> Kurt-Mothes-Str. 3
>> 06120 Halle/Saale
>>
>> Phone: +49-345-55-24942
>
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://sites.google.com/site/akohlmey/ Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:01 CST