From: The Cromicus Productions (thecromicusproductions_at_gmail.com)
Date: Mon Dec 25 2017 - 18:04:43 CST
I figured it out! This happened because I forgot to add the files
topology top_all36_na.rtf
topology top_all36_cgenff.rtf
topology top_all36_carb.rtf
Now it's working, thanks everyone and Merry Christmas!
On Mon, Dec 25, 2017 at 6:53 PM, The Cromicus Productions <
thecromicusproductions_at_gmail.com> wrote:
> I tried with "mutate" and looks like it ALMOST works, as I get the
> following error:
> psfgen) mutating residue 4 from ADE to 6MA
> psfgen) Info: generating structure...psfgen) unknown atom type HGA3
> psfgen) add atom failed in residue 6MA:1
> failed!
> ERROR: failed on end of segment
>
> On Mon, Dec 25, 2017 at 6:29 PM, The Cromicus Productions <
> thecromicusproductions_at_gmail.com> wrote:
>
>> Thanks for the replies! I know that it is defined as a residue, however,
>> I'm not very familiar with the force field files. My question was, is it
>> possible/easy to
>> define a patch that converts an A residue into a 6MA? If so, how can I do
>> that/learn to do that?
>>
>> I tried to add the following but get an error "psfgen) applying patch
>> M6NA to 1 residues
>> psfgen) unknown atom type HGA3
>> psfgen) add atom failed in patch M6NA
>> ERROR: failed to apply patch"
>>
>> PRES M6NA 0.00 ! patch for converting A into N6MA
>> ! use in PATCH statement followed by AUTOgenerate
>> ANGLes DIHE
>> GROUP
>> ATOM N9 NG2R51 -0.01 ! H61
>> ATOM C8 CG2R53 0.43 ! \
>> ATOM H8 HGR52 0.08 ! H62-CM6 H6
>> ATOM N7 NG2R50 -0.85 ! / \ /
>> ATOM C5 CG2RC0 0.32 ! H63 N6
>> ATOM C6 CG2R64 0.45 ! |
>> ATOM N6 NG311 -0.45 ! C6
>> ATOM H6 HGPAM1 0.33 ! // \
>> ATOM N1 NG2R62 -0.78 ! N1 C5--N7\\
>> ATOM C2 CG2R64 0.49 ! | || C8-H8
>> ATOM H2 HGR62 0.14 ! C2 C4--N9/
>> ATOM N3 NG2R62 -0.86 ! / \\ / \
>> ATOM C4 CG2RC0 0.52 ! H2 N3 \
>> ATOM CM6 CG331 -0.08 ! \
>> ATOM H61 HGA3 0.09 ! \
>> ATOM H62 HGA3 0.09 !
>> ATOM H63 HGA3 0.09 !
>> GROUP !
>> ATOM CM CG331 -0.27
>> ATOM HM1 HGA3 0.09
>> ATOM HM2 HGA3 0.09
>> ATOM HM3 HGA3 0.09
>>
>> BOND CM HM1 CM HM2 CM HM3
>> BOND N9 C8 N9 C4 C8 N7 C8 H8
>> BOND N7 C5 C5 C6 C5 C4 C6 N6
>> BOND C6 N1 N6 CM6 N6 H6 N1 C2
>> BOND C2 N3 C2 H2 N3 C4 CM6 H61
>> BOND CM6 H62 CM6 H63
>> BOND CM N9
>> IMPR C6 C5 N1 N6 ! N6 C6 CM6 H6
>> DONO H6 N6
>> ACCE N3
>> ACCE N7
>> ACCE N1
>> IC C8 C4 *N9 CM 1.3830 106.03 179.68 126.91 1.4740
>> IC C4 N9 C8 N7 1.3497 107.34 0.02 112.90 1.3249
>> IC N7 N9 *C8 H8 1.3249 112.90 -179.86 122.61 1.0947
>> IC N9 C8 N7 C5 1.3736 112.90 0.40 103.62 1.3989
>> IC C4 N7 *C5 C6 1.3954 110.25 -178.17 133.05 1.4051
>> IC N7 C5 C6 N1 1.3989 133.05 177.05 117.60 1.3793
>> IC N1 C5 *C6 N6 1.3793 117.60 179.99 122.23 1.3815
>> IC C5 C6 N6 CM6 1.4051 122.23 167.61 118.33 1.4832
>> IC CM6 C6 *N6 H6 1.4832 118.33 180.00 112.50 1.0190
>> IC C5 C6 N1 C2 1.4051 117.60 1.54 120.04 1.3647
>> IC C6 N1 C2 N3 1.3793 120.04 -1.14 125.07 1.3600
>> IC N3 N1 *C2 H2 1.3600 125.07 -179.44 117.43 1.0938
>> IC C6 N6 CM6 H61 1.3815 118.33 174.59 110.48 1.1123
>> IC H61 N6 *CM6 H62 1.1123 110.48 120.34 111.22 1.1126
>> IC H61 N6 *CM6 H63 1.1123 110.48 -119.06 111.26 1.1131
>>
>> On Mon, Dec 25, 2017 at 10:17 AM, Lennart Nilsson <Lennart.Nilsson_at_ki.se>
>> wrote:
>>
>>> This residue is defined as a complete residue (RESI 6MA) and not as a
>>> patch; in this file patches are mainly used for alternative tautomers or
>>> protonation states. Just check the supplementary information of the JCC
>>> paper, or why not simply have look at the file you are trying to use –
>>> “toppar_all36_na_rna_modified.str” is a human-readable text file, and
>>> it is quite clear that 6MA is a RESIdue and not a patch (PRES):
>>>
>>> toppar_all36_na_rna_modified.str:RESI 6MA -1.00 !
>>> N6-methyladenosine
>>>
>>>
>>>
>>> Good luck!
>>>
>>> Lennart Nilsson
>>>
>>>
>>>
>>> *From:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *On
>>> Behalf Of *The Cromicus Productions
>>> *Sent:* den 24 december 2017 10:49
>>> *To:* NAMD list <namd-l_at_ks.uiuc.edu>
>>> *Subject:* namd-l: [NAMD] Question about patches
>>>
>>>
>>>
>>> Hi everyone,
>>>
>>>
>>>
>>> I'm working with DNA and trying to convert an adenine group into an
>>>
>>> N6-methyladenosine. I found the force field from
>>>
>>>
>>> Xu, Y., K. Vanommeslaeghe, A. Aleksandrov, A. D. MacKerell and L.
>>> Nilsson (2016). "Additive CHARMM force field for naturally occurring
>>> modified ribonucleotides." Journal of Computational Chemistry 37: 896-912
>>>
>>>
>>>
>>> on one of the latest modifications of CHARMM36
>>> (toppar_all36_na_rna_modified.str) but I'm having problems because
>>> there is no patch defined to do this modification and I don't know how to
>>> define a patch. Could anyone lead me towards how to perform this task?
>>>
>>> I have succeeded before with other modifications such as methylating C
>>> bases, but I always had a patch defined in the force field to do this.
>>>
>>>
>>>
>>> Thank you very much and merry Christmas,
>>>
>>>
>>>
>>> Sebastian
>>>
>>
>>
>
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