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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- application/octet-stream attachment: STE.mol2
Received on Fri Jan 07 2022 - 14:00:02 PST
