Hello,
These problems arise, as Carlos said, because you're using different
atom types (lower case, which are gaff atom types) than those used for
the rest of the bases. The rest of the bases are "Amber" atom types
(and are thus upper-case). Therefore, at the phosphate bonds, where
your modified (d?)G is bonded to its neighbor, the clash of atom types
(gaff for modified base, Amber for neighbor) is unrecognized by leap.
Gaff was primarily designed for parameterizing non- covalently bonded
ligands.
There is an option in antechamber to specify Amber atom types, though
having never used it on nucleotides before, I don't know exactly how
well it works (i.e. whether it will be compatible with the way Amber
names nucleic acid atom types).
Another way you can fix this is to look at the atom types for
non-mutated G (you can find those in the OFF library file for nucleic
acids in $AMBERHOME/dat/leap/lib), and manually insert those into the
column for atom types in your prepin file (do not use your frcmod
file). You will of course have to find a new atom type for the O6
you're changing as well as an atom type for the new methyl group, but
these should not be too hard to find if you look at the appropriate
parm file (parm94.dat for ff99SB). Hopefully Antechamber will only
change the atom type of the affected atoms, so very few if any
parameters will be missing from ff99SB or whichever force field you're
using.
However, as Carlos said, you want to be careful when building the
parameter file, since it'll be quite easy to build a useless prmtop
with bogus parameters and not even realize it.
Good luck!
Jason
On Mon, Feb 1, 2010 at 6:53 AM, Carlos Simmerling
<carlos.simmerling.gmail.com> wrote:
> it looks to me like your problem is that you used lower case atom types.
> since normal DNA is upper case types, you need all of the terms
> defined for the connection between your mod G and the other DNA.
> you will have to be very careful doing this- and also make SURE to
> duplicate the dihedral terms for DNA in your frcmod. you haven't done
> this, which means that your G backbone and glycosidic angle will not
> behave correctly. you want to make sure that differences between the
> mod G and real G are from the O6-me, not from things that you didn't
> put in properly.
> to summarize, what I mean is that even if you don't get errors I think
> this looks incorrect.
>
>
> On Mon, Feb 1, 2010 at 6:47 AM, N.R. Jena <nrjena.gmail.com> wrote:
>> Dear All,
>> I have a non standard residue where guanine has been modified to
>> O6-methylguanine. I have treated it in antechamber and created 1.prepin and
>> 1.frcmod files as follows. However, while uploading all these files along
>> with the original .pdb file in .tleap, it is unable to save the final .top
>> and .crd files. I guess there is somewhere connectivity problem but unable
>> to trace it. It will be extremely helpful if someone can trace the problem
>> and help to solve this.
>>
>> PS: While saving the .top file it is asking for some strange parameters (!)
>> as given below (extreme last).
>>
>> With regards,
>> -N R Jena.
>>
>> 1.prepin:
>> -----------------------------------------------------------------------
>> This is a remark line
>> molecule.res
>> 6OG � �INT �0
>> CORRECT � � OMIT DU � BEG
>> �0.0000
>> � 1 �DUMM �DU � �M � �0 �-1 �-2 � � 0.000 � � �.0 � � � �.0 � � �.00000
>> � 2 �DUMM �DU � �M � �1 � 0 �-1 � � 1.449 � � �.0 � � � �.0 � � �.00000
>> � 3 �DUMM �DU � �M � �2 � 1 � 0 � � 1.522 � 111.1 � � � �.0 � � �.00000
>> � 4 �O1P � o � � M � �3 � 2 � 1 � � 1.540 � 111.208 � 180.000 �-0.67935
>> � 5 �P � � p4 � �M � �4 � 3 � 2 � � 1.497 � �63.191 �-135.455 � 1.65250
>> � 6 �O2P � o � � E � �5 � 4 � 3 � � 1.497 � 119.708 � �21.487 �-0.74911
>> � 7 �O5' � os � �M � �5 � 4 � 3 � � 1.597 � 109.514 � 147.148 �-0.56330
>> � 8 �C5' � c3 � �M � �7 � 5 � 4 � � 1.421 � 119.746 �-121.132 � 0.15117
>> � 9 �H69 � h1 � �E � �8 � 7 � 5 � � 1.000 � 109.202 � -37.427 � 0.05306
>> �10 �H71 � h1 � �E � �8 � 7 � 5 � � 1.000 � 109.222 � �82.273 � 0.05662
>> �11 �C4' � c3 � �M � �8 � 7 � 5 � � 1.505 � 110.455 �-157.571 � 0.00155
>> �12 �C3' � c3 � �3 � 11 � 8 � 7 � � 1.512 � 112.078 � �43.751 � 0.46165
>> �13 �C2' � c3 � �B � 12 �11 � 8 � � 1.511 � 102.985 � -88.669 �-0.18552
>> �14 �H65 � hc � �E � 13 �12 �11 � � 1.000 � 111.386 � �82.647 � 0.04195
>> �15 �H67 � hc � �E � 13 �12 �11 � � 1.000 � 111.400 �-154.782 � 0.06635
>> �16 �O3' � o � � E � 12 �11 � 8 � � 1.403 � 108.374 � 154.249 �-0.80798
>> �17 �H77 � h1 � �E � 12 �11 � 8 � � 0.999 � 114.615 � �34.033 �-0.21291
>> �18 �H73 � h1 � �E � 11 � 8 � 7 � � 1.000 � 106.429 � 164.996 � 0.07584
>> �19 �O4' � os � �M � 11 � 8 � 7 � � 1.437 � 109.349 � -72.096 �-0.43132
>> �20 �C1' � c3 � �M � 19 �11 � 8 � � 1.411 � 110.610 � 109.014 � 0.25931
>> �21 �H75 � h2 � �E � 20 �19 �11 � � 1.000 � 114.970 � 105.868 � 0.08448
>> �22 �N9 � �na � �M � 20 �19 �11 � � 1.457 � 107.744 �-136.937 �-0.25723
>> �23 �C4 � �ca � �M � 22 �20 �19 � � 1.364 � 125.447 �-105.290 � 0.46631
>> �24 �N3 � �nb � �M � 23 �22 �20 � � 1.347 � 125.709 � �-0.536 �-0.75225
>> �25 �C2 � �ca � �M � 24 �23 �22 � � 1.311 � 111.850 � 179.249 � 0.86736
>> �26 �N2 � �nh � �B � 25 �24 �23 � � 1.340 � 119.615 �-179.595 �-0.90689
>> �27 �H57 � hn � �E � 26 �25 �24 � � 1.000 � 109.483 � �59.993 � 0.39800
>> �28 �H59 � hn � �E � 26 �25 �24 � � 1.000 � 109.506 � -59.991 � 0.40479
>> �29 �N1 � �nb � �M � 25 �24 �23 � � 1.370 � 123.482 � � 0.358 �-0.83893
>> �30 �C6 � �ca � �M � 29 �25 �24 � � 1.391 � 125.193 � �-0.104 � 0.72532
>> �31 �O6 � �os � �S � 30 �29 �25 � � 1.349 � 120.111 � 179.623 �-0.42270
>> �32 �C � � c3 � �3 � 31 �30 �29 � � 1.426 � 120.207 � � 0.154 � 0.12447
>> �33 �H49 � h1 � �E � 32 �31 �30 � � 1.000 � 109.472 � 179.992 � 0.05312
>> �34 �H51 � h1 � �E � 32 �31 �30 � � 1.000 � 109.481 � �60.009 � 0.03628
>> �35 �H53 � h1 � �E � 32 �31 �30 � � 1.000 � 109.476 � -59.984 � 0.04086
>> �36 �C5 � �ca � �M � 30 �29 �25 � � 1.389 � 111.731 � �-0.335 �-0.19892
>> �37 �N7 � �nc � �M � 36 �30 �29 � � 1.382 � 130.273 �-179.431 �-0.54803
>> �38 �C8 � �cd � �M � 37 �36 �30 � � 1.304 � 104.220 � 179.991 � 0.43144
>> �39 �H55 � h5 � �E � 38 �37 �36 � � 1.000 � 123.508 � 179.741 � 0.10202
>> LOOP
>> �C1' �C2'
>> � C8 � N9
>> � C5 � C4
>>
>> IMPROPER
>> �C1' � C4 � N9 � C8
>> � C5 � N9 � C4 � N3
>> � N3 � N1 � C2 � N2
>> � C2 �H57 � N2 �H59
>> � C5 � N1 � C6 � O6
>> � C4 � C6 � C5 � N7
>> �H55 � N9 � C8 � N7
>>
>> DONE
>> STOP
>>
>> 1.frcmod
>> -----------------------------------------------------------------------------
>> remark goes here
>> MASS
>>
>> BOND
>>
>> ANGLE
>> c3-c3-o � �62.686 � � 116.465 � Calculated with empirical approach
>> nb-ca-os � 72.377 � � 119.785 � Calculated with empirical approach
>>
>> DIHE
>>
>> IMPROPER
>> c3-ca-na-cd � � � � 1.1 � � � � �180.0 � � � � 2.0 � � � � �Using default
>> value
>> ca-na-ca-nb � � � � 1.1 � � � � �180.0 � � � � 2.0 � � � � �Using default
>> value
>> nb-nb-ca-nh � � � � 1.1 � � � � �180.0 � � � � 2.0 � � � � �Using default
>> value
>> ca-hn-nh-hn � � � � 1.1 � � � � �180.0 � � � � 2.0 � � � � �Using default
>> value
>> ca-nb-ca-os � � � � 1.1 � � � � �180.0 � � � � 2.0 � � � � �Using default
>> value
>> ca-ca-ca-nc � � � � 1.1 � � � � �180.0 � � � � 2.0 � � � � �Using default
>> value
>> h5-na-cd-nc � � � � 1.1 � � � � �180.0 � � � � 2.0 � � � � �Using default
>> value
>>
>> NONBON
>>
>> --------------------------------------------------------------
>> Error in .tleap
>>
>> Building topology.
>> Building atom parameters.
>> Building bond parameters.
>> Could not find bond parameter for: OS - o
>> Could not find bond parameter for: cd - P
>> Building angle parameters.
>> Could not find angle parameter: OS - o - p4
>> Could not find angle parameter: CT - OS - o
>> Could not find angle parameter: h5 - cd - P
>> Could not find angle parameter: cd - P - O2
>> Could not find angle parameter: cd - P - O2
>> Could not find angle parameter: cd - P - OS
>> Could not find angle parameter: nc - cd - P
>> Could not find angle parameter: na - cd - P
>> Building proper torsion parameters.
>> �** No torsion terms for �OS-o-p4-o
>> �** No torsion terms for �OS-o-p4-os
>> �** No torsion terms for �CT-OS-o-p4
>> �** No torsion terms for �h5-cd-P-O2
>> �** No torsion terms for �h5-cd-P-O2
>> �** No torsion terms for �h5-cd-P-OS
>> �** No torsion terms for �nc-cd-P-O2
>> �** No torsion terms for �nc-cd-P-O2
>> �** No torsion terms for �nc-cd-P-OS
>> �** No torsion terms for �na-cd-P-O2
>> �** No torsion terms for �na-cd-P-O2
>> �** No torsion terms for �na-cd-P-OS
>> Building improper torsion parameters.
>> old PREP-specified impropers:
>> �<6OG 7>: �C1' �C4 � N9 � C8
>> �<6OG 7>: �C5 � N9 � C4 � N3
>> �<6OG 7>: �N3 � N1 � C2 � N2
>> �<6OG 7>: �C2 � H57 �N2 � H59
>> �<6OG 7>: �C5 � N1 � C6 � O6
>> �<6OG 7>: �C4 � C6 � C5 � N7
>> �<6OG 7>: �H55 �N9 � C8 � N7
>> �total 610 improper torsions applied
>> �7 improper torsions in old prep form
>> Building H-Bond parameters.
>> Parameter file was not saved.
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Feb 01 2010 - 05:00:03 PST
