Ok, I just wrote a quick script to replace numbers and move things
around.... generated a mol2 to check connectivity, so i guess manually is
ok
I now have an MHP lib file with the following order:
!!index array str
"MHP"
!entry.MHP.unit.atoms table str name str type int typex int resx int
flags int seq int elmnt dbl chg
"N" "N" 0 1 131072 1 7 -0.347900
"H" "H" 0 1 131072 2 1 0.274700
"CA" "CX" 0 1 131072 3 6 -0.135400
"HA" "H1" 0 1 131072 4 1 0.121200
"CB" "CT" 0 1 131072 5 6 -0.041400
"HB2" "HC" 0 1 131072 6 1 0.081000
"HB3" "HC" 0 1 131072 7 1 0.081000
"CG" "CC" 0 1 131072 8 6 -0.001200
"ND1" "NA" 0 1 131072 9 7 -0.151300
"CE1" "CR" 0 1 131072 11 6 -0.017000
"HE1" "H5" 0 1 131072 12 1 0.268100
"NE2" "NA" 0 1 131072 13 7 -0.171800
"HE2" "H" 0 1 131072 14 1 0.391100
"CD2" "CW" 0 1 131072 15 6 -0.114100
"HD2" "H4" 0 1 131072 16 1 0.231700
"C" "C" 0 1 131072 17 6 0.734100
"O" "O" 0 1 131072 18 8 -0.589400
"HD1" "H" 0 1 131072 10 1 0.386600
!entry.MHP.unit.atomspertinfo table str pname str ptype int ptypex int
pelmnt dbl pchg
"N" "N" 0 -1 0.0
"H" "H" 0 -1 0.0
"CA" "CX" 0 -1 0.0
"HA" "H1" 0 -1 0.0
"CB" "CT" 0 -1 0.0
"HB2" "HC" 0 -1 0.0
"HB3" "HC" 0 -1 0.0
"CG" "CC" 0 -1 0.0
"ND1" "NA" 0 -1 0.0\
"CE1" "CR" 0 -1 0.0
"HE1" "H5" 0 -1 0.0
"NE2" "NA" 0 -1 0.0
"HE2" "H" 0 -1 0.0
"CD2" "CW" 0 -1 0.0
"HD2" "H4" 0 -1 0.0
"C" "C" 0 -1 0.0
"O" "O" 0 -1 0.0
"HD1" "H" 0 -1 0.0
!entry.MHP.unit.boundbox array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.MHP.unit.childsequence single int
2
!entry.MHP.unit.connect array int
1
16
!entry.MHP.unit.connectivity table int atom1x int atom2x int flags
1 2 1
1 3 1
3 4 1
3 5 1
3 16 1
5 6 1
5 7 1
5 8 1
8 9 1
8 14 1
9 18 1
9 10 1
10 11 1
10 12 1
12 13 1
12 14 1
14 15 1
16 17 1
!entry.MHP.unit.hierarchy table str abovetype int abovex str belowtype
int belowx
"U" 0 "R" 1
"R" 1 "A" 1
"R" 1 "A" 2
"R" 1 "A" 3
"R" 1 "A" 4
"R" 1 "A" 5
"R" 1 "A" 6
"R" 1 "A" 7
"R" 1 "A" 8
"R" 1 "A" 9
"R" 1 "A" 10
"R" 1 "A" 11
"R" 1 "A" 12
"R" 1 "A" 13
"R" 1 "A" 14
"R" 1 "A" 15
"R" 1 "A" 16
"R" 1 "A" 17
"R" 1 "A" 18
!entry.MHP.unit.name single str
"MHP"
!entry.MHP.unit.positions table dbl x dbl y dbl z
3.325770 1.547909 -1.607204E-06
3.909407 0.723611 -2.739882E-06
3.970048 2.845795 -1.311163E-07
3.671663 3.400129 -0.889820
3.576965 3.653838 1.232143
2.496995 3.801075 1.241379
3.877484 3.115795 2.131197
4.200813 5.026064 1.321087
3.942782 5.885086 2.382972
4.624274 6.997642 2.182500
4.563048 7.811875 2.904563
5.294011 6.891451 1.061663
5.896297 7.605085 0.676854
5.058974 5.678868 0.492453
5.537741 5.417846 -0.451343
5.485541 2.705207 -4.398755E-06
6.008824 1.593175 -8.449768E-06
3.339725 5.691913 3.169805
!entry.MHP.unit.residueconnect table int c1x int c2x int c3x int c4x
int c5x int c6x
1 16 0 0 0 0
!entry.MHP.unit.residues table str name int seq int childseq int
startatomx str restype int imagingx
"MHP" 1 19 1 "p" 0
!entry.MHP.unit.residuesPdbSequenceNumber array int
0
!entry.MHP.unit.solventcap array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.MHP.unit.velocities table dbl x dbl y dbl z
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
I have moved MD1 to the end of the residue template, as that is the only
atom which is different from HIE. Is this the correct approach for setting
up single topology?
Drew
On Thu, Dec 14, 2017 at 10:03 AM, Andrew Schaub <aschaub.uci.edu> wrote:
> 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 <(949)%20824-8829> (lab)
> 949-877-9380 <(949)%20877-9380> (cell)
> aschaub.uci.edu <http://www.linkedin.com/pub/andrew-schaub/9a/907/382/>
>
>
--
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/>
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Received on Thu Dec 14 2017 - 10:30:04 PST
