That should help, thank you!
-Hunter
-----Original Message-----
>From: Daniel Roe <daniel.r.roe.gmail.com>
>Sent: Aug 8, 2013 3:29 PM
>To: AMBER Mailing List <amber.ambermd.org>
>Subject: Re: [AMBER] Suggestions for using "distance" in cpptraj
>
>Hi,
>
>You can test mask selections in cpptraj with the "parminfo" or
>"select" commands. This is easiest to do in interactive mode. For
>example:
>
>> parminfo :7
>#Atom Name #Res Name #Mol Type Charge Mass
> 105 N 7 GLY 1 N -0.4157 14.0100
> 106 H 7 GLY 1 H 0.2719 1.0080
> 107 CA 7 GLY 1 CT -0.0252 12.0100
> 108 HA2 7 GLY 1 H1 0.0698 1.0080
> 109 HA3 7 GLY 1 H1 0.0698 1.0080
> 110 C 7 GLY 1 C 0.5973 12.0100
> 111 O 7 GLY 1 O -0.5679 16.0000
>
>> parminfo .CA
>#Atom Name #Res Name #Mol Type Charge Mass
> 5 CA 1 SER 1 CT 0.0567 12.0100
> 16 CA 2 TRP 1 CT -0.0275 12.0100
> 40 CA 3 THR 1 CT -0.0389 12.0100
> 54 CA 4 TRP 1 CT -0.0275 12.0100
> 78 CA 5 GLU 1 CT 0.0397 12.0100
> 93 CA 6 ASN 1 CT 0.0143 12.0100
> 107 CA 7 GLY 1 CT -0.0252 12.0100
> 114 CA 8 LYS 1 CT -0.2400 12.0100
> 136 CA 9 TRP 1 CT -0.0275 12.0100
> 160 CA 10 THR 1 CT -0.0389 12.0100
> 174 CA 11 TRP 1 CT -0.0275 12.0100
> 198 CA 12 LYS 1 CT -0.2400 12.0100
>
>> select .CA
>Selected 12 atoms.
>Selected= 5 16 40 54 78 93 107 114 136 160 174 198
>
>You can also test mask selections in parmed.py and with ambmask.
>
>Hope this helps,
>
>-Dan
>
>On Thu, Aug 8, 2013 at 2:44 PM, Hunter Brown <bassoongoon.earthlink.net> wrote:
>> Hello, I am wanting to use cpptraj for some distance analysis (using the distance command). I want to see how far my ligand is from a specific residue. What is a good way for me to pick one residue, and to be certain that it is the residue I want? I know that amber numbers residues in numerical order.
>>
>> Thanks in advance!
>> -Hunter
>>
>> Hunter Brown
>> Bassoonist, Contrabassoonist, Composer, Chemical Engineering Major
>> University of New Mexico
>>
>> _______________________________________________
>> 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
Hunter Brown
Bassoonist, Contrabassoonist, Composer, Chemical Engineering Major
University of New Mexico
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Received on Thu Aug 08 2013 - 15:00:03 PDT
