Dear Jason, I am giving the full output-------------
| Run on 06/05/2015 at 21:57:31
[-O]verwriting output
File Assignments:
| MDIN: avg-min1.in
| MDOUT: avg-min1_test.out
|INPCRD: average.rst7
| PARM: 1ehz_asl.prmtop
|RESTRT: average_new.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
|
Here is the input file:
&cntrl
imin=1, maxcyc=100,
ntmin=2, cut=8.0, ntb=1
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
| peek_ewald_inpcrd: Box info not found in inpcrd
~
~
"avg-min1_test.out" 43L, 2219C
1,0-1 All
---------------------------------------------------------------------
Indrajit Deb
Kolkata, India.
Mob: +919239202278
On Fri, Jun 5, 2015 at 10:04 PM, Indrajit Deb <biky2004indra.gmail.com>
wrote:
> Dear Jason,
>
> Thanks for the information. The cpptraj command worked.
> But the problem is that, when I am using this newly prepared rst7 file as
> an input coordinate (-c average.rst7), sander giving the following
> error-------------
>
> | peek_ewald_inpcrd: Box info not found in inpcrd
>
> What should I do now ?
>
> Dear Kenneth, I have already tried as you recommended and it worked.
>
> Thanks
>
> ----indrajit
>
>
>
>
>
>
>
> ---------------------------------------------------------------------
> Indrajit Deb
> Kolkata, India.
> Mob: +919239202278
>
> On Fri, Jun 5, 2015 at 9:19 PM, Kenneth Huang <kennethneltharion.gmail.com
> > wrote:
>
>> Indrajit,
>>
>> VMD should be able to save the pdb as a rst file- I'm not sure if amber
>> has
>> that utility, or if there's other options. Alternatively, you could just
>> use your average pdb as an input in tleap to make a new topology and
>> coordinate file to run in sander.
>>
>> Best,
>>
>> Kenneth
>>
>> On Fri, Jun 5, 2015 at 11:26 AM, Indrajit Deb <biky2004indra.gmail.com>
>> wrote:
>>
>> > Dear amber users,
>> >
>> > I have a average pdb file which have short contacts. I want to convert
>> the
>> > average pdb file into rst file, so that I can use it as an input for
>> > sander. Actually I want to energy minimize the average pdb.
>> >
>> > So how to convert average pdb file into rst file ?
>> >
>> > Thanks
>> >
>> > ----indrajit
>> >
>> >
>> >
>> >
>> > ---------------------------------------------------------------------
>> > Indrajit Deb
>> > Kolkata, India.
>> > Mob: +919239202278
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Ask yourselves, all of you, what power would hell have if those imprisoned
>> here could not dream of heaven?
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Fri Jun 05 2015 - 10:00:02 PDT
