RE: [NAMD] Question about patches

From: Lennart Nilsson (
Date: Tue Dec 26 2017 - 04:43:30 CST

For completeness:
You first have to delete atom H61, which in the canonical ADE residue is bonded to N6; if you don’t do this, the bonds, angles and dihedrals that are associated with H61 will be kept.

You should also check that you have the expected total charge and number of atoms, bonds, angles, impropers and dihedrals when you apply the patch. Not always easy, but in this case you can compare with what you get with RESI 6MA – and you can even compare energies.

Best wishes,
Lennart Nilsson

From: [] On Behalf Of The Cromicus Productions
Sent: den 26 december 2017 01:05
To: The Cromicus Productions <>
Subject: Re: namd-l: [NAMD] Question about patches

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 <<>> 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
ERROR: failed on end of segment

On Mon, Dec 25, 2017 at 6:29 PM, The Cromicus Productions <<>> 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
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 !
ATOM CM CG331 -0.27
ATOM HM1 HGA3 0.09
ATOM HM2 HGA3 0.09
ATOM HM3 HGA3 0.09

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
IMPR C6 C5 N1 N6 ! N6 C6 CM6 H6
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 <<>> 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:<> [<>] On Behalf Of The Cromicus Productions
Sent: den 24 december 2017 10:49
To: NAMD list <<>>
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,


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