Attachments available until Jul 20, 2024
I’m now getting back to some work from a few months ago. I’m trying to run per residue RMSD for an enzyme variant that I had MD data for.
I can’t seem to get the masks set up correctly, or at least I think that’s the problem. The variant has an insertion from residues 27-67 compared to WT. I believe the masks should therefore be 2-26, 68-228 (it starts at 2 because the s26_2n4s numbering starts at 2 since it’s missing the N-terminal Met but the reference 3k47.pdb file numbering starts at 1.)
The trajectory processing shows no atoms selected for reference residues 1, 27-67 (not expected), and 187-228 (expected). 'No atoms selected for reference residues 27-67' is not expected because those atoms should be excluded in the target (s26_2n4s), not the reference (3k47).
I have attached all of the relevant files.
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7.4 MB
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2.11 GB
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8.3 MB
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180 KB
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10 KB
Here are my commands:
cpptraj
parm s26_2n4s.prmtop
trajin mdcrd_s26_2n4s.nc
parm 3k47.pdb
reference 3k47.pdb parm 3k47.pdb [WTmDHFR]
rmsd ToWTmDHFR2 ref [WTmDHFR] :2-26,
68-228.CA :
1-186.CA perres perresmask :2-26,
68-228.CA perresout rmsd_s26_2n4s_3k47_by_res.dat perresavg rmsd_s26_2n4s_3k47_avg_by_res.dat
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 's26_2n4s.prmtop' (1 actions):
0: [rmsd ToWTmDHFR2 ref [WTmDHFR] :2-26,
68-228.CA :
1-186.CA perres perresmask :2-26,
68-228.CA perresout rmsd_s26_2n4s_3k47_by_res.dat perresavg rmsd_s26_2n4s_3k47_avg_by_res.dat]
Target mask: [:2-26,68-228.CA](186)
Reference topology: 3k47.pdb
Reference mask: [:1-186.CA](186)
Warning: No atoms selected for reference residue 1
Warning: No atoms selected for reference residue 27
Warning: No atoms selected for reference residue 28
Warning: No atoms selected for reference residue 29
Warning: No atoms selected for reference residue 30
Warning: No atoms selected for reference residue 31
Warning: No atoms selected for reference residue 32
Warning: No atoms selected for reference residue 33
Warning: No atoms selected for reference residue 34
Warning: No atoms selected for reference residue 35
Warning: No atoms selected for reference residue 36
Warning: No atoms selected for reference residue 37
Warning: No atoms selected for reference residue 38
Warning: No atoms selected for reference residue 39
Warning: No atoms selected for reference residue 40
Warning: No atoms selected for reference residue 41
Warning: No atoms selected for reference residue 42
Warning: No atoms selected for reference residue 43
Warning: No atoms selected for reference residue 44
Warning: No atoms selected for reference residue 45
Warning: No atoms selected for reference residue 46
Warning: No atoms selected for reference residue 47
Warning: No atoms selected for reference residue 48
Warning: No atoms selected for reference residue 49
Warning: No atoms selected for reference residue 50
Warning: No atoms selected for reference residue 51
Warning: No atoms selected for reference residue 52
Warning: No atoms selected for reference residue 53
Warning: No atoms selected for reference residue 54
Warning: No atoms selected for reference residue 55
Warning: No atoms selected for reference residue 56
Warning: No atoms selected for reference residue 57
Warning: No atoms selected for reference residue 58
Warning: No atoms selected for reference residue 59
Warning: No atoms selected for reference residue 60
Warning: No atoms selected for reference residue 61
Warning: No atoms selected for reference residue 62
Warning: No atoms selected for reference residue 63
Warning: No atoms selected for reference residue 64
Warning: No atoms selected for reference residue 65
Warning: No atoms selected for reference residue 66
Warning: No atoms selected for reference residue 67
Warning: No atoms selected for reference residue 187
Warning: No atoms selected for reference residue 188
Warning: No atoms selected for reference residue 189
The written per-residue output appears to be correct up until residue 187. I think there should be data written for target residues 187-228
ACTION OUTPUT:
RMSD: Per-residue: Writing data for 228 residues to rmsd_s26_2n4s_3k47_by_res.dat
TIME: Analyses took 0.0000 seconds.
DATASETS (231 total):
ToWTmDHFR2 "ToWTmDHFR2" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:1 "MET:1" (double, rms), size is 0
ToWTmDHFR2[res]:2 "VAL:2" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:3 "ARG:3" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:4 "PRO:4" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:5 "LEU:5" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:6 "ASN:6" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:7 "CYS:7" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:8 "ILE:8" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:9 "VAL:9" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:10 "ALA:10" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:11 "VAL:11" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:12 "SER:12" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:13 "GLN:13" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:14 "ASN:14" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:15 "MET:15" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:16 "GLY:16" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:17 "ILE:17" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:18 "GLY:18" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:19 "LYS:19" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:20 "ASN:20" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:21 "GLY:21" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:22 "ASP:22" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:23 "LEU:23" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:24 "PRO:24" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:25 "TRP:25" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:26 "PRO:26" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:27 "SER:27" (double, rms), size is 0
ToWTmDHFR2[res]:28 "GLY:28" (double, rms), size is 0
ToWTmDHFR2[res]:29 "GLY:29" (double, rms), size is 0
ToWTmDHFR2[res]:185 "GLU:185" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:186 "SER:186" (double, rms), size is 4406 (35.248 kB)
ToWTmDHFR2[res]:187 "ASP:187" (double, rms), size is 0
ToWTmDHFR2[res]:188 "THR:188" (double, rms), size is 0
ToWTmDHFR2[res]:189 "PHE:189" (double, rms), size is 0
ToWTmDHFR2[res]:190 "PHE:190" (double, rms), size is 0
ToWTmDHFR2[res]:191 "PRO:191" (double, rms), size is 0
ToWTmDHFR2[res]:192 "GLU:192" (double, rms), size is 0
ToWTmDHFR2[res]:193 "ILE:193" (double, rms), size is 0
ToWTmDHFR2[res]:194 "ASP:194" (double, rms), size is 0
ToWTmDHFR2[res]:195 "LEU:195" (double, rms), size is 0
ToWTmDHFR2[res]:196 "GLY:196" (double, rms), size is 0
ToWTmDHFR2[res]:197 "LYS:197" (double, rms), size is 0
ToWTmDHFR2[res]:198 "TYR:198" (double, rms), size is 0
ToWTmDHFR2[res]:199 "LYS:199" (double, rms), size is 0
ToWTmDHFR2[res]:200 "LEU:200" (double, rms), size is 0
ToWTmDHFR2[res]:201 "LEU:201" (double, rms), size is 0
ToWTmDHFR2[res]:202 "PRO:202" (double, rms), size is 0
ToWTmDHFR2[res]:203 "GLU:203" (double, rms), size is 0
ToWTmDHFR2[res]:204 "TYR:204" (double, rms), size is 0
ToWTmDHFR2[res]:205 "PRO:205" (double, rms), size is 0
ToWTmDHFR2[res]:206 "GLY:206" (double, rms), size is 0
ToWTmDHFR2[res]:207 "VAL:207" (double, rms), size is 0
ToWTmDHFR2[res]:208 "LEU:208" (double, rms), size is 0
ToWTmDHFR2[res]:209 "SER:209" (double, rms), size is 0
ToWTmDHFR2[res]:210 "GLU:210" (double, rms), size is 0
ToWTmDHFR2[res]:211 "VAL:211" (double, rms), size is 0
ToWTmDHFR2[res]:212 "GLN:212" (double, rms), size is 0
ToWTmDHFR2[res]:213 "GLU:213" (double, rms), size is 0
ToWTmDHFR2[res]:214 "GLU:214" (double, rms), size is 0
ToWTmDHFR2[res]:215 "LYS:215" (double, rms), size is 0
ToWTmDHFR2[res]:216 "GLY:216" (double, rms), size is 0
ToWTmDHFR2[res]:217 "ILE:217" (double, rms), size is 0
ToWTmDHFR2[res]:218 "LYS:218" (double, rms), size is 0
ToWTmDHFR2[res]:219 "TYR:219" (double, rms), size is 0
ToWTmDHFR2[res]:220 "LYS:220" (double, rms), size is 0
ToWTmDHFR2[res]:221 "PHE:221" (double, rms), size is 0
ToWTmDHFR2[res]:222 "GLU:222" (double, rms), size is 0
ToWTmDHFR2[res]:223 "VAL:223" (double, rms), size is 0
ToWTmDHFR2[res]:224 "TYR:224" (double, rms), size is 0
ToWTmDHFR2[res]:225 "GLU:225" (double, rms), size is 0
ToWTmDHFR2[res]:226 "LYS:226" (double, rms), size is 0
ToWTmDHFR2[res]:227 "LYS:227" (double, rms), size is 0
ToWTmDHFR2[res]:228 "ASP:228" (double, rms), size is 0
ToWTmDHFR2[Avg] "ToWTmDHFR2[Avg]" (X-Y mesh), size is 228 (3.648 kB) ToWTmDHFR2[Stdev] "ToWTmDHFR2[Stdev]" (X-Y mesh), size is 228 (3.648 kB)
Lastly, the Datafiles section appears to be correct, except for residues 187-228 where again, there is no data.
DATAFILES (2 total):
rmsd_s26_2n4s_3k47_by_res.dat (Standard Data File): MET:1 VAL:2 ARG:3 PRO:4 ... GLU:225 LYS:226 LYS:227 ASP:228
rmsd_s26_2n4s_3k47_avg_by_res.dat (Standard Data File): ToWTmDHFR2[Avg] ToWTmDHFR2[Stdev]
Warning: Set 'MET:1' contains no data.
Warning: Set 'SER:27' contains no data.
Warning: Set 'GLY:28' contains no data.
Warning: Set 'GLY:29' contains no data.
Warning: Set 'ALA:30' contains no data.
Warning: Set 'THR:31' contains no data.
Warning: Set 'ALA:32' contains no data.
Warning: Set 'VAL:33' contains no data.
Warning: Set 'SER:34' contains no data.
Warning: Set 'GLU:35' contains no data.
Warning: Set 'TRP:36' contains no data.
Warning: Set 'THR:37' contains no data.
Warning: Set 'GLU:38' contains no data.
Warning: Set 'TYR:39' contains no data.
Warning: Set 'LYS:40' contains no data.
Warning: Set 'THR:41' contains no data.
Warning: Set 'ALA:42' contains no data.
Warning: Set 'ASP:43' contains no data.
Warning: Set 'GLY:44' contains no data.
Warning: Set 'LYS:45' contains no data.
Warning: Set 'THR:46' contains no data.
Warning: Set 'TYR:47' contains no data.
Warning: Set 'TYR:48' contains no data.
Warning: Set 'TYR:49' contains no data.
Warning: Set 'ASN:50' contains no data.
Warning: Set 'ASN:51' contains no data.
Warning: Set 'ARG:52' contains no data.
Warning: Set 'THR:53' contains no data.
Warning: Set 'GLU:54' contains no data.
Warning: Set 'GLU:55' contains no data.
Warning: Set 'SER:56' contains no data.
Warning: Set 'THR:57' contains no data.
Warning: Set 'TRP:58' contains no data.
Warning: Set 'GLU:59' contains no data.
Warning: Set 'LYS:60' contains no data.
Warning: Set 'PRO:61' contains no data.
Warning: Set 'GLN:62' contains no data.
Warning: Set 'GLU:63' contains no data.
Warning: Set 'LEU:64' contains no data.
Warning: Set 'LYS:65' contains no data.
Warning: Set 'GLY:66' contains no data.
Warning: Set 'SER:67' contains no data.
Warning: Set 'ASP:187' contains no data.
Warning: Set 'THR:188' contains no data.
Warning: Set 'PHE:189' contains no data.
Warning: Set 'PHE:190' contains no data.
Warning: Set 'PRO:191' contains no data.
Warning: Set 'GLU:192' contains no data.
Warning: Set 'ILE:193' contains no data.
Warning: Set 'ASP:194' contains no data.
Warning: Set 'LEU:195' contains no data.
Warning: Set 'GLY:196' contains no data.
Warning: Set 'LYS:197' contains no data.
Warning: Set 'TYR:198' contains no data.
Warning: Set 'LYS:199' contains no data.
Warning: Set 'LEU:200' contains no data.
Warning: Set 'LEU:201' contains no data.
Warning: Set 'PRO:202' contains no data.
Warning: Set 'GLU:203' contains no data.
Warning: Set 'TYR:204' contains no data.
Warning: Set 'PRO:205' contains no data.
Warning: Set 'GLY:206' contains no data.
Warning: Set 'VAL:207' contains no data.
Warning: Set 'LEU:208' contains no data.
Warning: Set 'SER:209' contains no data.
Warning: Set 'GLU:210' contains no data.
Warning: Set 'VAL:211' contains no data.
Warning: Set 'GLN:212' contains no data.
Warning: Set 'GLU:213' contains no data.
Warning: Set 'GLU:214' contains no data.
Warning: Set 'LYS:215' contains no data.
Warning: Set 'GLY:216' contains no data.
Warning: Set 'ILE:217' contains no data.
Warning: Set 'LYS:218' contains no data.
Warning: Set 'TYR:219' contains no data.
Warning: Set 'LYS:220' contains no data.
Warning: Set 'PHE:221' contains no data.
Warning: Set 'GLU:222' contains no data.
Warning: Set 'VAL:223' contains no data.
Warning: Set 'TYR:224' contains no data.
Warning: Set 'GLU:225' contains no data.
Warning: Set 'LYS:226' contains no data.
Warning: Set 'LYS:227' contains no data.
Warning: Set 'ASP:228' contains no data.
Please let me know how I can solve this issue.
Best regards,
Colin Pierce
Postdoctoral Associate
Daniel Schmidt Lab
University of Minnesota
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Received on Thu Jun 20 2024 - 08:00:02 PDT
