Apparently you lack superhuman memory and make mistakes too, not unlike
the rest of us, so I suggest you start over from scratch, copy fresh
canonical files, and create your own custom ones to debug. You may have
trashed real data, since you've been changing canonical files and don't
know what you're doing. If not yourself, think of the poor postdoc in a
concentration camp 10 years from now who is forced to replicate your
flawed results.
Bill
On 10/9/19 1:54 AM, Dawid das wrote:
> Yes, it works when I don't have SYN and I use original files.
> I must have messed something up while adding SYN definition.
>
> Thank you for guiding me!
>
> Best regards,
> Dawid Grabarek
>
> wt., 8 paź 2019 o 21:01 Carlos Simmerling <carlos.simmerling.gmail.com>
> napisał(a):
>
>> I think it's safest to put extra parameters into a new frcmod file instead
>> of modifying the original.
>> does it work when you don't have the SYN? you'll need to debug whether the
>> problem is from the modifications or from some other issue.
>>
>> On Tue, Oct 8, 2019 at 2:58 PM Dawid das <addiw7.googlemail.com> wrote:
>>
>>> Well, the only modifications I have introduced are regarding the new
>>> parameters for a SYN unit
>>> that I defined. They must be defined somewhere because SYN is an integral
>>> part of my protein.
>>>
>>> wt., 8 paź 2019 o 20:47 Carlos Simmerling <carlos.simmerling.gmail.com>
>>> napisał(a):
>>>
>>>> I also noticed that your parm99.dat is heavily modified compared to the
>>>> standard one. I would suggest using an actual parm99.dat from the Amber
>>>> distribution and see if that helps.
>>>>
>>>>
>>>> On Tue, Oct 8, 2019 at 2:00 PM Dawid das <addiw7.googlemail.com>
>> wrote:
>>>>> Dear Carlos,
>>>>>
>>>>> Thank you for letting me know. It was from one of my previous test
>>> runs.
>>>>> I attach a correct log.
>>>>>
>>>>> Best wishes,
>>>>> Dawid
>>>>>
>>>>> wt., 8 paź 2019 o 19:33 Carlos Simmerling <
>> carlos.simmerling.gmail.com
>>>>> napisał(a):
>>>>>
>>>>>> for some reason in your leap.log file I see this:
>>>>>> #parm99 = loadamberparams parm99.dat
>>>>>>
>>>>>> it isn't that way in the files you sent though. do you know why
>> this
>>>> line
>>>>>> was commented? parm99.dat has the vdw parameters.
>>>>>>
>>>>>> On Tue, Oct 8, 2019 at 12:04 PM Dawid das <addiw7.googlemail.com>
>>>> wrote:
>>>>>>> Dear Amber Users,
>>>>>>>
>>>>>>> I am trying to generate topology and parameters files for a
>> protein
>>>>>>> containing my own amino acid (unit).
>>>>>>>
>>>>>>> I attach my tleap.in, PDB and leap.log files together with some
>>>>>> parameter
>>>>>>> files I use as the input.
>>>>>>>
>>>>>>> The issue is that I get an error saying that vdW parameters are
>>>> missing
>>>>>>> for virtually every atom even though I can see them correctly
>>> defined
>>>>>>> in leaprc.ff99SBildn and parm99.dat. What could be the problem?
>>>>>>>
>>>>>>> Best regards,
>>>>>>> Dawid Grabarek
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Received on Wed Oct 09 2019 - 02:30:02 PDT
