Hi Lizelle,
I guess the suspicious behavior is not because of the indexes are different if you have them have the same LJ parameters.
It may be because of the issue raised by the bonded model, you can check the last paragraph in this webpage: http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm> for that issue.
-Pengfei
> On Aug 31, 2017, at 3:45 AM, Lizelle Lubbe <LBBLIZ002.myuct.ac.za> wrote:
>
> Hi David,
>
> Thanks for the advice last week. I was not aware of the difference in LJ parameter units in AMBER.
> When checking the validity of a dry prmtop in parmed.py it says *.prmtop looks OK to me! The TIP3P waters are thus to blame.
>
> My system contains a water coordinated to ZN. When printing the LJ types I noticed that the oxygen of the active site water is type index 20 whereas all the other TIP3p OW atoms are LJ type index 23. In parmed I can set the radius and well depth to new values but these are equivalent for type 20 and 23.
>
> Is there any way to change the type index from 20 to 23?
> The water behaviour during minimization is suspect and I just want to confirm that this is not the cause.
>
> Kind regards
>
> Lizelle Lubbe
>
> PhD (Medical biochemistry) candidate
> Department of Integrative Biomedical Sciences
> University of Cape Town
> ________________________________________
> From: David A Case <david.case.rutgers.edu>
> Sent: 25 August 2017 10:17:08 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] TIP3p lennard jones parameters
>
> On Fri, Aug 25, 2017, Lizelle Lubbe wrote:
>
>> I noticed that the TIP3P parameters in this file do not correspond to
>> the literature (radius 3.15061; well depth 0.6364)
>> My values are 1.7683 and 0.1520 respectively.
>
> Your "literature" values are sigma (in Å) and epsilon (in kJ/mol). Amber
> uses Rmin/2 (in Å) and epsilon in kcal/mol. If you convert to what
> Amber uses, you will find that they match.
>
>>
>> If not, how can I increase the verbosity in parmed.py to come to the
>> bottom of this?
>
> I agree that there are situations where it would be quite helpful if
> parmed could print more information when it finds problems. Volunteers
> are hereby solicited.
>
>>
>>
>> source leaprc.ff14SB
>
> General advice: upgrade to AmberTools17. Second, if you think that your
> water model might be leading to off-diagonal LJ parms, do some exploring:
> make a prmtop with just water (for example), and see what parmed says. Keep
> adding in components one by one to see if you can isolate the problem.
>
> ...good luck....dac
>
>
>
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Received on Mon Sep 11 2017 - 09:30:04 PDT
