Dear Thomas,
I looked at the sustiva mol2 file at:
amber11/AmberTools/test/antechamber/sustiva/sustiva.mol2.save
.<TRIPOS>ATOM
1 C1 0.7280 1.4030 0.2550 ca 1 SUS -0.053000
2 H1 -0.1360 1.7560 0.7820 ha 1 SUS 0.170000
3 C2 0.8030 0.0800 -0.1500 ca 1 SUS -0.175300
4 C3 -0.2900 -0.9320 0.1580 c3 1 SUS 0.314200
5 C4 -1.6350 -0.3520 0.0320 c1 1 SUS -0.204100
6 C5 -2.7180 0.1230 -0.0620 c1 1 SUS 0.013900
7 C6 -4.0440 0.6950 -0.1770 cx 1 SUS -0.082600
8 H2 -4.7410 0.3350 0.5580 hc 1 SUS 0.103700
9 C7 -4.6000 1.0130 -1.5410 cx 1 SUS -0.108400 ! CH2
10 H3 -5.6460 0.8200 -1.6970 hc 1 SUS 0.077700 !
11 H4 -3.9750 0.8060 -2.3900 hc 1 SUS 0.085700 !
12 C8 -4.2070 2.1230 -0.6290 cx 1 SUS -0.107400 ! CH2
13 H5 -4.9810 2.6990 -0.1550 hc 1 SUS 0.077700 !
14 H6 -3.3140 2.6760 -0.8580 hc 1 SUS 0.086700 !
15 C9 -0.1170 -1.5000 1.5820 c3 1 SUS 0.626900
16 F1 1.0560 -2.0970 1.6930 f 1 SUS -0.227300 ! F
17 F2 -0.1700 -0.5360 2.4800 f 1 SUS -0.231300 ! F
18 F3 -1.0470 -2.3800 1.8660 f 1 SUS -0.214300 ! F
19 O1 -0.2320 -2.0480 -0.7120 os 1 SUS -0.378900
20 C10 0.8930 -2.5380 -1.2450 c 1 SUS 0.843600
21 O2 0.9220 -3.6240 -1.7130 o 1 SUS -0.582500
22 N1 1.9640 -1.6960 -1.2420 n 1 SUS -0.474100
23 H7 2.7760 -2.0540 -1.6920 hn 1 SUS 0.356500
24 C11 1.9190 -0.3690 -0.8360 ca 1 SUS 0.107600
25 C12 2.9630 0.5030 -1.1140 ca 1 SUS -0.172000
26 H8 3.8260 0.1540 -1.6530 ha 1 SUS 0.149000
27 C13 2.8920 1.8170 -0.7000 ca 1 SUS -0.068000
28 H9 3.6970 2.4940 -0.9110 ha 1 SUS 0.156000
29 C14 1.7720 2.2620 -0.0180 ca 1 SUS -0.017600
30 Cl1 1.6780 3.9240 0.4950 cl 1 SUS -0.074400
As you can see the charges values of the two methylene carbons in the
cyclopropane are not made equivalent. Same remarks for the 4
corresponding hydrogens. The same problem appends with the three
fluorine atoms.
In a force field library chemically equivalent atoms should bear the
same charge values.
-> I ran a R.E.D. Server job to create a P2N file using Ante_R.E.D. 2.0;
See
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFnhJllOncADFuQN0l7NwQYTIVV4yADFOBqiADF/P5625.html
& the corresponding Java applet:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFnhJllOncADFuQN0l7NwQYTIVV4yADFOBqiADF/P5625/javaappletp2n-1.html
As you can see chemically equivalent atoms bear the same names.
-> Then, I ran a R.E.D. Server job to create a mol2 file using R.E.D. IV;
See
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFhOylaxqlADFzL4Cysxvl0I8LQUnNOgvDADF/P5626.html
& the corresponding Java applet:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFhOylaxqlADFzL4Cysxvl0I8LQUnNOgvDADF/P5626/javaappletmol2-1.html
the charge values are below:
.<TRIPOS>ATOM
1 C1 1.272707 0.955037 0.218065 C 1 SUS -0.0833
2 H1 0.667412 1.669187 0.740410 H 1 SUS 0.1348
3 C2 0.726981 -0.251449 -0.190703 C 1 SUS 0.1337
4 C3 -0.713385 -0.639467 0.107326 C 1 SUS 0.0264
5 C4 -1.633630 0.498422 -0.024389 C 1 SUS -0.0403
6 C5 -2.372588 1.421684 -0.123572 C 1 SUS -0.0849
7 C6 -3.281058 2.543349 -0.244382 C 1 SUS -0.0389
8 H2 -4.069960 2.548010 0.486222 H 1 SUS 0.1540
9 C7 -3.617299 3.083921 -1.609973 C 1 SUS -0.2724 !
10 H3 -4.632466 3.397908 -1.772595 H 1 SUS 0.1481 !
11 H4 -3.153965 2.610440 -2.455804 H 1 SUS 0.1481 !
12 C8 -2.760424 3.884858 -0.692970 C 1 SUS -0.2724 !
13 H5 -3.181938 4.754077 -0.221172 H 1 SUS 0.1481 !
14 H6 -1.711558 3.960269 -0.914470 H 1 SUS 0.1481 !
15 C9 -0.833576 -1.222878 1.529780 C 1 SUS 0.3258
16 F1 -0.072197 -2.296582 1.645725 F 1 SUS -0.1183 !
17 F2 -0.439491 -0.345337 2.430940 F 1 SUS -0.1183 !
18 F3 -2.067504 -1.571307 1.805843 F 1 SUS -0.1183 !
19 O1 -1.174838 -1.654669 -0.766210 O 1 SUS -0.3190
20 C10 -0.401963 -2.611523 -1.294219 C 1 SUS 0.8602
21 O2 -0.877655 -3.585757 -1.765921 O 1 SUS -0.6015
22 N1 0.937096 -2.362538 -1.281874 N 1 SUS -0.5161
23 H7 1.492564 -3.057687 -1.727694 H 1 SUS 0.3411
24 C11 1.511098 -1.166593 -0.872077 C 1 SUS 0.1589
25 C12 2.842944 -0.880443 -1.140784 C 1 SUS -0.2912
26 H8 3.448306 -1.589314 -1.676193 H 1 SUS 0.1962
27 C13 3.386938 0.316443 -0.722580 C 1 SUS -0.0541
28 H9 4.416196 0.541803 -0.926848 H 1 SUS 0.1585
29 C14 2.597717 1.231397 -0.046264 C 1 SUS -0.0523
30 Cl1 3.282700 2.746547 0.472091 CL 1 SUS -0.1011
As you can charge values are correctly equivalenced, and quite different...
regards, Francois
Quoting Thomas Pochapsky <pochapsk.brandeis.edu>:
> Thanks to Ben for your help; antechamber in AmberTools 1.5 is
> running fine, the sustiva example works. Now I am trying to get it
> to work for my molecule. I am trying to parameterize a macrocyclic
> lactone antibiotic for Leap, and based on the ATOMTYPE.INF file, the
> atoms are being identified and bonded correctly, but the
> antechamber run fails at the sqm step. sqm.out says that there is
> no convergence in SCF after 1000 steps.
>
> So I guess I have several questions that I couldn't find answers for
> from the manual or paper.
>
> 1) "Bond types are assigned for valence state 14 with a penalty of
> 2. " From Fig. 5 in the paper, penalty of 2 looks good, but I
> couldn't figure out where the value of 14 comes from (formula is C37
> H59 O11 N).
>
> 2) Atoms in the macrolactone ring are not identified as being in a
> ring, I assume this was because rings are only 3,4,5 and 6 member?
>
> 3) Can I increase the number of steps in the SCF run to see if that
> gives convergence? Failing that, can I force output of a .mol2
> file to see where the problems lie, or this info in one of the
> files I already get?
>
> Thanks again,
>
> Tom Pochapsky
>
>
> On Jan 9, 2012, at 1:24 PM, Ben Roberts wrote:
>
>> Hi Tom,
>>
>> On 9/01/2012, at 1:15 PM, Thomas Pochapsky wrote:
>>
>>> I am new to antechamber, I am trying to parameterize a macrocyclic
>>> compound, and am unable to get atom types or even coordinates in
>>> my output files, even using the sustiva_h.pdb tutorial example.
>>> It looks like a path problem to me, but Amber runs OK, so should I
>>> have additional lines in my .cshrc so that antechamber finds the
>>> parameters it is looking for?
>>>
>>> I am providing the input line I used from the tutorial, and the output.
>>>
>>> input:> antechamber -i sustiva_h-1.pdb -fi pdb -o sustiva_h.mol2
>>> -fo mol2 -c bcc -s 2
>>>
>>> output:
>>> Running: /nmr/Programs/amber/amber8/exe/atomtype -i
>>> ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
>>>
>>> Total number of electrons: 160; net charge: 0
>>>
>>> Running: /nmr/Programs/amber/amber8/exe/divcon
>>>
>>> Running: /nmr/Programs/amber/amber8/exe/am1bcc -i
>>> ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
>>> /nmr/Programs/amber/amber8/dat/antechamber/BCCPARM.DAT -j 4
>>>
>>> Cannot successfully assign bond type for this molecule, please :
>>> (1) double check the structure (the connectivity) and/or
>>> (2) adjust atom valence penalty parameters in APS.DAT, and/or
>>> (3) increase MAXVASTATE in define.h and recompile bondtype.C
>>
>> I see you're still using Amber 8. Antechamber has been re-released
>> a number of times since then, now as part of AmberTools, a free
>> download from http://ambermd.org. You may wish to download
>> AmberTools 1.5 (the most recent version) and try its antechamber.
>>
>> Regards,
>> Ben
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Received on Thu Jan 12 2012 - 13:00:03 PST
