Hello,
I think there is an error in tiMerge in parmed.
I wanted to evaluate the effect of a mutation (Phe->Tyr) on the binding of a ligand to a protein.
First I created a pdb file of the united wt and mutant molecules, created a parm7 and processed it with tiMerge. All looks fine up to this stage with the correct timask printed as output.
Then I did the same for the protein with the ligand, IPP. The initial parm7 looks OK but when I do the tiMerge, the timask it prints is incorrect.
Here is the timask:
timask1='.1658,1659,1660,1661,1662,1663,1664,1665,1666,1667,1668,1669,1670,1671,1672,1673,1674,1675,1676,1677',
timask2='.3009,3010,3011,3012,3013,3014,3015,3016,3017,3018,3019,3020,3021,3022,3023,3024,3025,3026,3027,3028,3029',
scmask1='.1658,1659,1660,1661,1662,1663,1664,1665,1666,1667,1668,1669,1670,1671,1672,1673,1674,1675,1676,1677',
scmask2='.3009,3010,3011,3012,3013,3014,3015,3016,3017,3018,3019,3020,3021,3022,3023,3024,3025,3026,3027,3028,3029',
timask1 is OK as you can see from the pdb file of the converted merged rst7
ATOM 1658 N PHE 104 43.348 38.930 42.247 1.00 0.00 N
ATOM 1659 H PHE 104 43.831 39.817 42.259 1.00 0.00 H
ATOM 1660 CA PHE 104 42.416 38.692 41.059 1.00 0.00 C
.
.
.
ATOM 1676 C PHE 104 43.173 38.705 39.716 1.00 0.00 C
ATOM 1677 O PHE 104 43.793 39.676 39.294 1.00 0.00 O
But timask2 is incorrect: It starts with atom 3009, but in the pdb (and parm7) it is 2986; the end is also not correct 3029 instead on 3006.
ATOM 2986 N TYR 187 43.348 38.930 42.247 1.00 0.00 N
ATOM 2987 H TYR 187 43.831 39.817 42.259 1.00 0.00 H
ATOM 2988 CA TYR 187 42.416 38.692 41.059 1.00 0.00 C
.
.
.
ATOM 3005 C TYR 187 43.173 38.705 39.716 1.00 0.00 C
ATOM 3006 O TYR 187 43.793 39.676 39.294 1.00 0.00 O
The atom 3009-3029 are part of the ligand IPP
ATOM 3007 P IPP 188 36.508 50.103 38.405 1.00 0.00 P
ATOM 3008 P1 IPP 188 37.296 47.893 36.900 1.00 0.00 P
ATOM 3009 O IPP 188 35.823 50.243 39.853 1.00 0.00 O
ATOM 3010 O1 IPP 188 37.001 48.666 38.228 1.00 0.00 O
.
.
.
ATOM 3027 H6 IPP 188 32.011 45.897 40.662 1.00 0.00 H
ATOM 3028 H7 IPP 188 32.089 49.511 40.893 1.00 0.00 H
ATOM 3029 H8 IPP 188 31.181 47.981 41.241 1.00 0.00 H
It looks to me like the ligand should be before TYR 187.
Here is the merge.in that I used:
loadRestrt btn3a1_ipp_f2y.rst7
setOverwrite True
tiMerge :1-187 :188-374 :104 :291
outparm btn3a1_ipp_merged.parm7 btn3a1_ipp_merged.rst7
outPDB btn3a1_ipp_merged.pdb
quit
I could provide additional files if needed for testing.
Thanks for your help.
Roman Osman
Professor
Department of Pharmacological Sciences
Icahn School of Medicine at Mount Sinai
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Received on Fri Mar 03 2023 - 10:00:02 PST
