Ambertools 16 is free. Please use it, there are lots of enhancements
Hai
> On Nov 17, 2016, at 9:39 AM, ABHIJEET CHOWDHURY <f2013854.pilani.bits-pilani.ac.in> wrote:
>
> Dear David,
>
> Thank you for the information. Yes, indeed I am using AMBER 10 and so this
> might be the case. Is there any other way to create a pdb format other than
> using a newer version of AMBER.
>
> Regards,
> Abhijeet
>
> On Thu, Nov 17, 2016 at 7:15 PM, David A Case <david.case.rutgers.edu>
> wrote:
>
>>> On Thu, Nov 17, 2016, ABHIJEET CHOWDHURY wrote:
>>>
>>> I want to convert my coordinate file generated into pdb format for
>>> nuparm but unable to find the right tool. I tried using ptraj but was
>>> unsuccessful. Although it created a pdb format but nuparm dose not
>>> accepts it as .pdb.
>>
>> Use cpptraj or ambpdb from AmberTools16: these adhere more closely to
>> the standard PDB format than does the (very old) ptraj program. Use the
>> -bres flag to have residue names in the output PDB file match those in PDB
>> standard.
>>
>> [Note: this may not work, since it looks(?) like you created the Amber
>> files
>> with an old version of the program that still used residue names like "RA"
>> for
>> adenosine (rather than the correct "A"). If ambpdb with the -bres flag
>> doesn't make the name "A", you will have to edit the files to make that
>> change
>> yourself.]
>>
>> ...dac
>>
>>
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>>
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Received on Thu Nov 17 2016 - 07:00:03 PST
