On Thu, Dec 17, 2015 at 7:39 AM, Kenneth Huang
<kennethneltharion.gmail.com> wrote:
> strip WAT:Na+
Actually this is a malformed atom mask. The correct mask would be :
:WAT,Na+
-Dan
>
> To remove the extra stuff, and put it after you load your trajectory and
> before you write the output.
>
> Best,
>
> Kenneth
>
>
> On Thursday, December 17, 2015, shahab shariati <shahab.shariati.gmail.com>
> wrote:
>
>> Dear amber users
>>
>> My system contains protein (residues 1-314) + ligand (residue 315) + Na
>> ions (residues 316-323) + water molecules.
>>
>> After doing MD simulation using amber tools 14, I have 4000 frames.
>>
>> Now, I need to a trajectory containing only protein + ligand molecules
>> (residues 1-315) and only frames 3950 and 4000.
>>
>> I have runned cpptraj in batch mode using following in files:
>>
>> parm comp_sol.prmtop
>> trajin trajectory.binpos 3950 4000
>> trajout 6.pdb pdb :1-315
>>
>> parm comp_sol.prmtop
>> trajin trajectory.binpos 3950 4000 :1-315
>> trajout 6.pdb pdb
>>
>> But both cases give me a trajectory in which there are protein + ligand +
>> Na + water molecules instead of only protein + ligand molecules.
>>
>> How to do what I want.
>>
>> Any help will highly appreciated
>> _______________________________________________
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>> 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?
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--
-------------------------
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
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Received on Thu Dec 17 2015 - 07:30:03 PST
