Re: [AMBER] add_pdb

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 25 Apr 2012 21:36:47 -0400

The point was that ambpdb might be compatible with a chamber topology file that's made to be compatible with VMD. Therefore, use chamber to generate a topology file that is consistent with VMD, then use that topology file to generate your pdb with ambpdb (don't forget to use add_pdb first).

HTH,
Jason

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Apr 25, 2012, at 8:39 PM, colvin <colvin4367.gmail.com> wrote:
> 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 - 19:00:09 PDT