If I use tleap:
> MHP = HIP
> saveoff MHP MHP.lib
Creating MHP.lib
Saving MHP.
Building topology.
Building atom parameters.
> quit
My MHP residue has the HD1 atom in the middle, and not after CO. Is there
an easy way to edit the lib file to move it to the end?
On Thu, Dec 14, 2017 at 9:58 AM, Andrew Schaub <aschaub.uci.edu> wrote:
> How do I set this up? Looking at the tutorial, I assuming as follows:
> 1) Leave the original PDB untouched
> 2) Create a lib file for HIP (as I can't use the one from amber due to
> reordering)
> 3) Move the only atoms that are different between the two after the C and
> O atoms, in this case it is the delta protin (HD1).
>
> In the first PDB I have:
>
> ATOM 3920 N HIE 252 27.329 52.218 59.744 1.00
> 0.00 N
> ATOM 3921 H HIE 252 26.567 52.021 59.111 1.00
> 0.00 H
> ATOM 3922 CA HIE 252 27.688 51.188 60.699 1.00
> 0.00 C
> ATOM 3923 HA HIE 252 28.775 51.117 60.665 1.00
> 0.00 H
> ATOM 3924 CB HIE 252 27.031 51.445 62.092 1.00
> 0.00 C
> ATOM 3925 HB2 HIE 252 27.106 52.494 62.377 1.00
> 0.00 H
> ATOM 3926 HB3 HIE 252 25.971 51.206 62.005 1.00
> 0.00 H
> ATOM 3927 CG HIE 252 27.688 50.670 63.233 1.00
> 0.00 C
> ATOM 3928 ND1 HIE 252 29.010 50.292 63.429 1.00
> 0.00 N
> ATOM 3930 CE1 HIE 252 29.103 49.910 64.747 1.00
> 0.00 C
> ATOM 3931 HE1 HIE 252 30.023 49.700 65.273 1.00
> 0.00 H
> ATOM 3932 NE2 HIE 252 27.856 49.834 65.234 1.00
> 0.00 N
> ATOM 3933 HE2 HIE 252 27.688 49.538 66.185 1.00
> 0.00 H
> ATOM 3934 CD2 HIE 252 26.935 50.410 64.358 1.00
> 0.00 C
> ATOM 3935 HD2 HIE 252 25.919 50.739 64.521 1.00
> 0.00 H
> ATOM 3936 C HIE 252 27.342 49.765 60.174 1.00
> 0.00 C
> ATOM 3937 O HIE 252 26.324 49.560 59.539 1.00
> 0.00 O
>
> In the second PDB I have:
>
> ATOM 3920 N MHP 252 27.329 52.218 59.744 1.00
> 0.00 N
> ATOM 3921 H MHP 252 26.567 52.021 59.111 1.00
> 0.00 H
> ATOM 3922 CA MHP 252 27.688 51.188 60.699 1.00
> 0.00 C
> ATOM 3923 HA MHP 252 28.775 51.117 60.665 1.00
> 0.00 H
> ATOM 3924 CB MHP 252 27.031 51.445 62.092 1.00
> 0.00 C
> ATOM 3925 HB2 MHP 252 27.106 52.494 62.377 1.00
> 0.00 H
> ATOM 3926 HB3 MHP 252 25.971 51.206 62.005 1.00
> 0.00 H
> ATOM 3927 CG MHP 252 27.688 50.670 63.233 1.00
> 0.00 C
> ATOM 3928 ND1 MHP 252 29.010 50.292 63.429 1.00
> 0.00 N
> ATOM 3930 CE1 MHP 252 29.103 49.910 64.747 1.00
> 0.00 C
> ATOM 3931 HE1 MHP 252 30.023 49.700 65.273 1.00
> 0.00 H
> ATOM 3932 NE2 MHP 252 27.856 49.834 65.234 1.00
> 0.00 N
> ATOM 3933 HE2 MHP 252 27.688 49.538 66.185 1.00
> 0.00 H
> ATOM 3934 CD2 MHP 252 26.935 50.410 64.358 1.00
> 0.00 C
> ATOM 3935 HD2 MHP 252 25.919 50.739 64.521 1.00
> 0.00 H
> ATOM 3936 C MHP 252 27.342 49.765 60.174 1.00
> 0.00 C
> ATOM 3937 O MHP 252 26.324 49.560 59.539 1.00
> 0.00 O
> *ATOM 3929 HD1 MHP 252 29.713 50.431 62.718 1.00
> 0.00 H *
>
> Is there an easy way to generate a lib file of my new HIP residue?
>
> Best Regards,
>
> Drew
>
--
Andrew Schaub
Graduate Program in Chemical & Structural Biology
Tsai Lab, http:///www.tsailabuci.com/ <http://www.tsailabuci.com/>
Luo Lab, http://rayl0.bio.uci.edu/html/
University of California, Irvine
Irvine, CA 92697-2280
949-824-8829 (lab)
949-877-9380 (cell)
aschaub.uci.edu <http://www.linkedin.com/pub/andrew-schaub/9a/907/382/>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Dec 14 2017 - 10:30:02 PST
