> On Apr 12, 2016, at 2:35 PM, Jun Feng <jufeng.mail.wvu.edu> wrote:
>
> Hi, Jason,
> I am able to use ParmEd to create prmtop file this time from the most
> recent CHARMM c36 force filed. But when I run pmemd.cuda, there was SHAKE
> problem:
> Number of triangulated 3-point waters found: 0
>
> There are supposed to have 7867 water. I do not know why water cannot be
> recognized in the prmtop file.
> I came with this solution to define water in the dyn.in
> file: watnam='TIP3',OWTNM='OH2', hwtnm1='H1',hwtnm2='H2',
> Then I am able to run the simulation.
> Is this solution OK?
This is correct.
>
> But I never have this problem using "old CHAMBER" to convert CHARMM
> generated psf to prmtop and run in pmemd.cuda. Pmemd.cuda was always able
> to recognize water molecules from "old Chamber" generated prmtop file.
> Any comment?
If this is true, the old chamber must have automatically renamed TIP3 to WAT and the TIP3 atom names to tleap's default naming convention. I doubt this would work for other water models like tip4p (if CHARMM uses or even supports those models).
HTH,
Jason
>
> Thanks!
>
>
> On Tue, Apr 12, 2016 at 10:27 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
>>
>>
>>> On Apr 11, 2016, at 1:18 PM, Jun Feng <jufeng.mail.wvu.edu> wrote:
>>>
>>> Hi,
>>>
>>> I use the most recent CHARMM force field downloaded from Dr. Mackerell's
>>> website named toppar_c36_feb16.tgz (a modified C36 protein parameter set)
>>> to generate psf. I tried to use CHAMBER to convert to AMBER format
>> prmtop.
>>> But I get the following error message from CHAMBER:
>>>
>>> CMAP Found
>>> Found 4 unique cmap types:
>>> Type: 1 - 16 36 19 16 36 19 16 36
>>> C NH1 CT1 C NH1 CT1 C NH1
>>>
>>> Type: 2 - 16 36 20 16 36 20 16 36
>>> C NH1 CT2 C NH1 CT2 C NH1
>>>
>>> Type: 3 - 16 36 19 16 36 19 16 33
>>> C NH1 CT1 C NH1 CT1 C N
>>>
>>> Type: 4 - 16 33 27 16 33 27 16 36
>>> C N CP1 C N CP1 C NH1
>>>
>>> ERROR: CMAP reading terminated reading entry 19 / 576
>>>
>>> This might be incompatibility between the new c36 force field with
>> modified
>>> CMAP and CHAMBER. Can the CHAMBER developers provide some help to this
>>> issue?
>>
>> The chamber program has been deprecated and removed from current versions
>> of Amber. Try using the chamber action in ParmEd instead.
>>
>> Just make sure you get the latest version of AmberTools (15 currently)
>> before trying it.
>>
>> You can find more details in the Amber 15 manual.
>>
>> You can also prepare your system in CHARMM-GUI, which will use ParmEd
>> internally to create the appropriate Amber files for you.
>>
>> I know ParmEd has been used a decent amount with CHARMM 36, so unless your
>> files are corrupted somehow, it should work.
>>
>> HTH,
>> Jason
>>
>>> Thanks!
>>>
>>>
>>> --
>>> Jun Feng
>>> Postdoc Fellow
>>> Blake Mertz Research Group
>>> Department of Chemistry
>>> West Virginia University
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> Jun Feng
> Postdoc Fellow
> Blake Mertz Research Group
> Department of Chemistry
> West Virginia University
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Apr 13 2016 - 04:00:04 PDT
