Hi,
The 'rst' command in cpptraj can convert regular Amber mask
expressions to Amber group format. For example:
> rst :1 :12 r1 2 r2 3.5 r3 3.5 r4 5 rk2 5 rk3 5
Mask [:1] corresponds to 13 atoms.
Mask [:12] corresponds to 22 atoms.
&rst iat=-1,-1,0
r1=2.000000, r2=3.500000, r3=3.500000, r4=5.000000, rk2=5.000000,
rk3=5.000000,
IGR1(1)=1,IGR1(2)=2,IGR1(3)=3,IGR1(4)=4,IGR1(5)=5,IGR1(6)=6,IGR1(7)=7,IGR1(8)=8,IGR1(9)=9,IGR1(10)=10,IGR1(11)=11,IGR1(12)=12,IGR1(13)=13,
IGR2(1)=196,IGR2(2)=197,IGR2(3)=198,IGR2(4)=199,IGR2(5)=200,IGR2(6)=201,IGR2(7)=202,IGR2(8)=203,IGR2(9)=204,IGR2(10)=205,IGR2(11)=206,IGR2(12)=207,IGR2(13)=208,IGR2(14)=209,IGR2(15)=210,IGR2(16)=211,IGR2(17)=212,IGR2(18)=213,IGR2(19)=214,IGR2(20)=215,IGR2(21)=216,IGR2(22)=217,
nstep1=0, nstep2=0,
&end
See the manual for full details.
-Dan
On Tue, Aug 29, 2017 at 8:56 AM, Suchetana Gupta <tutulg.gmail.com> wrote:
> Dear Amber users
> I want to perform umbrella sampling on my protein of interest. What will be
> the format for specifying the COM of certain residues (say I want to apply
> restraint on residues x to y)? I realised that I can manually write all the
> atom numbers using iat and igr, but is there any existing format to do it
> automatically? Also, is it true that the iat can read only upto 200 atoms
> at a time?
> Thanks in advance
> Suchetana Gupta
> IIT Madras
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Aug 29 2017 - 12:30:03 PDT
