Hi,
You could try the GitHub version of cpptraj, which has recently been
given the ability to write CONECT records to PDB files based on bond
information via the 'conect' keyword:
https://github.com/Amber-MD/cpptraj
Example input:
parm myparm.parm7
trajin mytraj.nc 1 1
trajout mypdb.pdb conect
Hope this helps,
-Dan
On Wed, Nov 4, 2015 at 11:21 PM, windy <chxp_moon.163.com> wrote:
> Thanks for you reply.
>
> I test the mol2 file and find out it can truely export the connection message, however when you try to convert it to the pdb (sybyl, Discovery Studio, and also obabel), the PDB format or connection records still lost a lot.
>
>
>
>
>
> 在2015年11月03 21时06分, "Jason Swails"<jason.swails.gmail.com>写道:
>
> On Mon, Nov 2, 2015 at 9:55 PM, windy <chxp_moon.163.com> wrote:
>
>> Hi, everyone,
>>
>> How do amber trajout pdb with connectivity records? Are there any
>> solutions?
>>
>
> There is no option for this in Amber right now.
>
>
>> For my trajectory has a user-defined new residue (like phosphorylation
>> and so on), when I trajout one frames to PDB (no connection records) and
>> furthur QM/MM calculation in Gaussian, the Gaussian software often judge
>> the wrong connection, especially the amino acid with benzene ring (PHE,
>> usually the 1.5 bonding and 2.0 bonding).
>>
>> I further using Discovery or Sybyl to read the original PDBs from Amber
>> to generate the connection records, but the connectivity records is
>> disruptted around the user-defined new residues (no complete connection
>> records generate).
>>
>> Are there any solutions to generate the complete connection records from
>> Amber?
>>
>
> Not that I know of.
>
> An idea might be to write a mol2 file (or something else that explicitly
> stores bonds), then see if a conversion program (maybe something like
> openbabel) will write a PDB file with CONECT records.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> 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
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Nov 05 2015 - 08:30:03 PST
