Hi,
Cpptraj and ptraj can both read PDBs. In order to use the hbond
command in cpptraj with PDB as parm you need to generate bond/mol info
(with bondsearch/molsearch keywords) since the PDB doesn't have it
(this will be done automatically in future releases of cpptraj). E.g.,
bondsearch
molsearch
parm input.pdb
trajin input.pdb
hbond .C,N,H,O avgout hbavg.dat
Ptraj doesn't need bond/mol info, but you need to manually specify
hbonding atoms with donor/acceptor keywords prior to the hbond
command. See the manual for more details.
Hope this was helpful,
-Dan
On Mon, Sep 17, 2012 at 11:41 PM, vaibhav dixit <vaibhavadixit.gmail.com> wrote:
> Can we do this with a pdb file? i.e. generate a list of pair of residue
> names/IDs between which there are backbone H-bond?
> Thanks for your suggestions.
>
> On Mon, Sep 17, 2012 at 6:08 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> Why not just use the hbond command? In cpptraj something like 'hbond
>> .C,N,H,O avgout hbavg.dat' should work.
>>
>> -Dan
>>
>> On Monday, September 17, 2012, vaibhav dixit wrote:
>>
>> > Dear Amber users,
>> > I'm using secstruct command for making secondary structure prediction.
>> > Manual says that it uses DSSP program. My question is...
>> > Can DSSP program be used to print a list of pair of AA residue names/IDs
>> > that form backbone H-bonds in a given protein sequence?
>> > It does seem to calculate/use this information for giving the usual
>> output
>> > files.
>> >
>> > Thanks for your help and suggestions in advance.
>> >
>> > --
>> > With regards
>> >
>> > Vaibhav A. Dixit
>> > Ph.D. Scholar
>> > Department of Medicinal Chemistry
>> > Natl. Inst. Pharm. Edu. & Res. (NIPER)
>> > Sector 67, Phase X, S.A.S. Nagar (Mohali)
>> > Punjab -160 062 INDIA
>> > Phone (Mobile): +919915214408
>> > E-mail: vaibhavadixit.gmail.com <javascript:;>
>> > www.niper.nic.in
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org <javascript:;>
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-9119 (Fax)
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> With regards
>
> Vaibhav A. Dixit
> Ph.D. Scholar
> Department of Medicinal Chemistry
> Natl. Inst. Pharm. Edu. & Res. (NIPER)
> Sector 67, Phase X, S.A.S. Nagar (Mohali)
> Punjab -160 062 INDIA
> Phone (Mobile): +919915214408
> E-mail: vaibhavadixit.gmail.com
> www.niper.nic.in
> _______________________________________________
> 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 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 18 2012 - 06:30:03 PDT
