Hi Dan,
I’m sorry; I’m not sure because I thought you load the mol2 into tleap and then use the head/tail/connect commands to specify how your new residue links up with other residues.
Perhaps someone else can jump in here and help out.
Best,
Matthew
> On Jan 7, 2022, at 5:17 PM, Daniel Konstantinovsky <daniel.konstantinovsky.yale.edu> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> 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 <mailto: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 - 17:00:02 PST
