Hi,
How does this relate to using the original residue numbering in the
prmtop file? I have no problem in generating pdb from chamber prmtop
and inpcrd using ptraj. I need to have prmtop file that using the same
original residue numbering for the protein. add_pdb does that but
ptraj couldn't read in the extra section and ambpdb is not compatible
with chamber prmtop, any other options that i can try?
Thanks and regards.
Colvin
On Thu, Apr 26, 2012 at 8:06 AM, Jason Swails <jason.swails.gmail.com> wrote:
> Chamber will optionally make a VMD-compatible topology file. Try using this topology instead
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
> On Apr 25, 2012, at 8:02 PM, colvin <colvin4367.gmail.com> wrote:
>
>> Hi,
>>
>> Thanks for the reply, but my prmtop file is actually generated from
>> chamber, i cannot use ambpdb to get pdb file because it gives me
>> error: ERROR: Flag "TITLE" not found in PARM file. Is there any other
>> workaround?
>>
>> Thanks and regards,
>> Colvin
>>
>>
>>
>> On Wed, Apr 25, 2012 at 8:26 PM, David A Case <case.biomaps.rutgers.edu> wrote:
>>> On Wed, Apr 25, 2012, colvin wrote:
>>>>
>>>> From the previous entry in amber archive, i came to know about this
>>>> program, add_pdb that add residue and atom information to the prmtop
>>>> file. I tried it and it did added in %FLAG RESIDUE_number in the new
>>>> prmtop file. I then used this new prmtop file to generate a pdb file,
>>>> (by traj in inpcrd file and traj out pdb) but the output pdb file does
>>>> not come with the original residue numbering, and it is numbered from
>>>> 1.
>>>
>>> Ptraj doesn't know anything about the extra sections in the prmtop file.
>>> Use ambpdb with the "-ext" flag to convert a prtmop/inpcrd file pair
>>> into a pdb file, making use of the extra information.
>>>
>>> ....dac
>>>
>>>
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Received on Wed Apr 25 2012 - 18:00:06 PDT
