Hi Matthew,
It does indeed work, but I noticed that in this file the bonding is
different (one of the atoms that's supposed to be bonded isn't).
It seems that the original bonding is rejected by tleap. I wonder if that's
because the residue is not valence-complete. It has an C-bound O atom that
I will later bond to a P, but right now it's just a dangling O bound to
C...Could that be it, and if so, what should I do?
Thank you!
Dan
On Fri, Jan 7, 2022 at 4:51 PM Matthew Guberman-Pfeffer <
matthew.guberman-pfeffer.uconn.edu> wrote:
> Dear Dan,
>
> I’m not sure what exactly is the problem, but I think it involves
> formatting again. How did you generate the mol2?
> Regardless, I have a hack-solution that you can try: I was able to save
> the contents you pasted into a plain text file and open it as a mol2 with
> Chimera. From there, I saved it as a mol2, and tleap read the
> Chimera-generated mol2 with no problem. I’ve attached this mol2 to this
> message. The downside is that you’ll need to add the charges back into the
> mol to by hand. it’s also possible that by comparing your mol2 and the
> Chimera-generated mol2, you can spot the problem tleap is having.
> Hope this helps.
>
>
> Best,
> Matthew
>
> > On Jan 7, 2022, at 3:18 PM, Daniel Konstantinovsky <
> daniel.konstantinovsky.yale.edu> wrote:
> >
> > *Message sent from a system outside of UConn.*
> >
> >
> > Hi Amber,
> >
> > I am trying to make a library file for a newly parameterized molecule and
> > when I try to read in the mol2 file in tleap it gives the following
> error:
> >
> > *Fatal Error: last line read: 1 STE 1 TEMP 0
> > **** **** 0 ROOT*
> >
> > I checked another mol2 file for another molecule that I know worked fine
> > and could see no differences. Just in case, my mol2 file is below. What
> > could be the problem here?
> >
> > Best,
> > Dan
> >
> > -----------------------------
> > .<TRIPos>MOLECULE
> > STE
> > 56 55 1 0 0
> > SMALL
> > rc
> >
> >
> > .<TRIPos>ATOM
> > 1 C1 5.6670 0.2230 1.0880 c2 0 STE
> > 0.174256
> > 2 O1 6.8790 -0.1280 0.4840 os 0 STE
> > -0.135727
> > 3 C2 4.9510 1.3070 0.2930 c2 0 STE
> > -1.197880
> > 4 C3 3.6300 1.7360 0.9340 c2 0 STE
> > 0.612643
> > 5 C4 2.9040 2.8180 0.1300 c2 0 STE
> > 0.360578
> > 6 C5 1.6220 3.3570 0.7780 c2 0 STE
> > -0.699197
> > 7 C6 0.4950 2.3420 1.0200 c2 0 STE
> > 0.587990
> > 8 C7 -0.0590 1.6990 -0.2540 c2 0 STE
> > 0.027946
> > 9 C8 -1.1740 0.6700 -0.0170 c2 0 STE
> > -0.418596
> > 10 C9 -2.4570 1.1820 0.6580 c2 0 STE
> > -0.163388
> > 11 C10 -3.1970 2.3130 -0.0750 c2 0 STE
> > -0.060784
> > 12 C11 -3.8250 1.9430 -1.4370 c2 0 STE
> > -0.098833
> > 13 C12 -5.3230 1.6110 -1.4020 c2 0 STE
> > 0.037374
> > 14 C13 -5.7090 0.3680 -0.5960 c2 0 STE
> > 0.033518
> > 15 C14 -7.2000 0.0370 -0.6940 c2 0 STE
> > -0.079155
> > 16 C15 -7.6000 -1.1980 0.1160 c2 0 STE
> > 0.003290
> > 17 C16 -9.0890 -1.5310 0.0170 c2 0 STE
> > 0.019089
> > 18 C17 -9.4910 -2.7660 0.8260 c2 0 STE
> > 0.107347
> > 19 C18 -10.9800 -3.0920 0.7220 c3 0 STE
> > -0.260141
> > 20 h1 4.7790 0.9200 -0.7040 hc 0 STE
> > 0.269146
> > 21 H2 5.6150 2.1640 0.2000 hc 0 STE
> > 0.269146
> > 22 H3 2.9900 0.8630 1.0390 hc 0 STE
> > -0.151956
> > 23 H4 3.8100 2.1050 1.9450 hc 0 STE
> > -0.151956
> > 24 H5 2.6910 2.4380 -0.8660 hc 0 STE
> > -0.071579
> > 25 H6 3.5820 3.6570 -0.0150 hc 0 STE
> > -0.071579
> > 26 H7 1.2310 4.1640 0.1590 hc 0 STE
> > 0.100082
> > 27 H8 1.8810 3.8110 1.7330 hc 0 STE
> > 0.100082
> > 28 H9 0.8400 1.5610 1.6940 hc 0 STE
> > -0.114763
> > 29 H10 -0.3060 2.8580 1.5450 hc 0 STE
> > -0.114763
> > 30 H11 0.7440 1.1900 -0.7780 hc 0 STE
> > 0.027265
> > 31 H12 -0.4070 2.4790 -0.9290 hc 0 STE
> > 0.027265
> > 32 H13 -1.4250 0.2130 -0.9700 hc 0 STE
> > 0.148580
> > 33 H14 -0.7750 -0.1340 0.5970 hc 0 STE
> > 0.148580
> > 34 H15 -2.2180 1.5290 1.6600 hc 0 STE
> > 0.052518
> > 35 H16 -3.1250 0.3360 0.7910 hc 0 STE
> > 0.052518
> > 36 H17 -3.9780 2.6950 0.5800 hc 0 STE
> > 0.040177
> > 37 H18 -2.5090 3.1400 -0.2160 hc 0 STE
> > 0.040177
> > 38 H19 -3.6960 2.7780 -2.1200 hc 0 STE
> > 0.028144
> > 39 H20 -3.2880 1.1120 -1.8860 hc 0 STE
> > 0.028144
> > 40 H21 -5.6660 1.4790 -2.4270 hc 0 STE
> > -0.009043
> > 41 H22 -5.8670 2.4700 -1.0110 hc 0 STE
> > -0.009043
> > 42 H23 -5.1280 -0.4840 -0.9470 hc 0 STE
> > 0.023397
> > 43 H24 -5.4460 0.5080 0.4490 hc 0 STE
> > 0.023397
> > 44 H25 -7.7810 0.8930 -0.3540 hc 0 STE
> > 0.012438
> > 45 H26 -7.4670 -0.1170 -1.7380 hc 0 STE
> > 0.012438
> > 46 H27 -7.3360 -1.0440 1.1610 hc 0 STE
> > -0.009252
> > 47 H28 -7.0170 -2.0530 -0.2210 hc 0 STE
> > -0.009252
> > 48 H29 -9.3550 -1.6870 -1.0280 hc 0 STE
> > -0.002846
> > 49 H30 -9.6740 -0.6760 0.3540 hc 0 STE
> > -0.002846
> > 50 H31 -8.9100 -3.6220 0.4900 hc 0 STE
> > -0.008537
> > 51 H32 -9.2280 -2.6120 1.8710 hc 0 STE
> > -0.008537
> > 52 H33 -11.2330 -3.9720 1.3060 hc 0 STE
> > 0.058829
> > 53 H34 -11.2670 -3.2860 -0.3080 hc 0 STE
> > 0.058829
> > 54 H35 -11.5890 -2.2680 1.0830 hc 0 STE
> > 0.058829
> > 55 H36 5.0230 -0.6420 1.1960 h1 0 STE
> > 0.152821
> > 56 H37 5.9010 0.5850 2.0870 h1 0 STE
> > 0.152821
> > .<TRIPos>BOND
> > 1 1 2 1
> > 2 1 3 1
> > 3 1 55 1
> > 4 1 56 1
> > 5 3 4 1
> > 6 3 20 1
> > 7 3 21 1
> > 8 4 5 1
> > 9 4 22 1
> > 10 4 23 1
> > 11 5 6 1
> > 12 5 24 1
> > 13 5 25 1
> > 14 6 7 1
> > 15 6 26 1
> > 16 6 27 1
> > 17 7 8 1
> > 18 7 28 1
> > 19 7 29 1
> > 20 8 9 1
> > 21 8 30 1
> > 22 8 31 1
> > 23 9 10 1
> > 24 9 32 1
> > 25 9 33 1
> > 26 10 11 1
> > 27 10 34 1
> > 28 10 35 1
> > 29 11 12 1
> > 30 11 36 1
> > 31 11 37 1
> > 32 12 13 1
> > 33 12 38 1
> > 34 12 39 1
> > 35 13 14 1
> > 36 13 40 1
> > 37 13 41 1
> > 38 14 15 1
> > 39 14 42 1
> > 40 14 43 1
> > 41 15 16 1
> > 42 15 44 1
> > 43 15 45 1
> > 44 16 17 1
> > 45 16 46 1
> > 46 16 47 1
> > 47 17 18 1
> > 48 17 48 1
> > 49 17 49 1
> > 50 18 19 1
> > 51 18 50 1
> > 52 18 51 1
> > 53 19 52 1
> > 54 19 53 1
> > 55 19 54 1
> > .<TRIPos>SUBSTRUCTURE
> > 1 STE 1 TEMP 0 **** **** 0 ROOT
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Received on Fri Jan 07 2022 - 14:30:03 PST
