Sure! Here is the NRQ.ac file:
CHARGE 0.00 ( 0 )
Formula: H17 C16 N3 O4 S1
ATOM 1 N1 NRQ 1 -0.910 2.155 0.064 -0.741100 N
ATOM 2 CE NRQ 1 -6.107 3.278 0.100 -0.046000 CT
ATOM 3 SD NRQ 1 -5.359 1.682 -0.327 -0.284200 S
ATOM 4 CG1 NRQ 1 -3.587 1.984 -0.087 -0.013300 CT
ATOM 5 CB1 NRQ 1 -2.804 0.711 -0.412 -0.120700 CT
ATOM 6 CA1 NRQ 1 -1.331 0.962 -0.212 0.411000 CM
ATOM 7 C1 NRQ 1 -0.372 -0.148 -0.332 0.336600 CK
ATOM 8 N2 NRQ 1 0.927 -0.014 -0.293 -0.556300 NB
ATOM 9 OH NRQ 1 6.539 2.591 0.550 -0.492100 OH
ATOM 10 CD2 NRQ 1 3.379 0.864 0.142 -0.051500 CA
ATOM 11 CE2 NRQ 1 4.282 1.859 0.384 -0.199000 CA
ATOM 12 CZ NRQ 1 5.647 1.597 0.310 0.151100 CA
ATOM 13 CE1 NRQ 1 6.101 0.321 -0.010 -0.199000 CA
ATOM 14 CD1 NRQ 1 5.208 -0.683 -0.253 -0.051500 CA
ATOM 15 CG2 NRQ 1 3.830 -0.426 -0.181 -0.129800 CA
ATOM 16 CB2 NRQ 1 2.868 -1.496 -0.440 0.044800 CD
ATOM 17 CA2 NRQ 1 1.512 -1.225 -0.431 -0.032600 CC
ATOM 18 C2 NRQ 1 0.413 -2.198 -0.569 0.681700 C
ATOM 19 O2 NRQ 1 0.510 -3.403 -0.715 -0.578500 O
ATOM 20 N3 NRQ 1 -0.723 -1.471 -0.494 -0.433300 N*
ATOM 21 CA3 NRQ 1 -2.089 -1.995 -0.580 0.069000 CT
ATOM 22 C3 NRQ 1 -2.602 -2.288 0.806 0.609100 C
ATOM 23 O3 NRQ 1 -1.900 -2.079 1.767 -0.552000 O
ATOM 24 OXT NRQ 1 -3.840 -2.779 0.974 -0.596100 OH
ATOM 25 H2 NRQ 1 0.027 2.303 0.266 0.432400 H
ATOM 26 HE1ANRQ 1 -5.861 3.531 1.131 0.062700 H1
ATOM 27 HE2ANRQ 1 -5.720 4.050 -0.566 0.062700 H1
ATOM 28 HE3 NRQ 1 -7.190 3.213 -0.010 0.062700 H1
ATOM 29 HG11NRQ 1 -3.263 2.789 -0.748 0.086200 H1
ATOM 30 HG12NRQ 1 -3.404 2.269 0.949 0.086200 H1
ATOM 31 HB11NRQ 1 -3.128 -0.093 0.249 0.074700 HC
ATOM 32 HB12NRQ 1 -2.987 0.426 -1.448 0.074700 HC
ATOM 33 HOH NRQ 1 6.804 2.666 1.478 0.424000 HO
ATOM 34 HD2 NRQ 1 2.320 1.067 0.204 0.150000 HA
ATOM 35 HE2 NRQ 1 3.937 2.851 0.633 0.147500 HA
ATOM 36 HE1 NRQ 1 7.161 0.125 -0.066 0.147500 HA
ATOM 37 HD1 NRQ 1 5.561 -1.673 -0.502 0.150000 HA
ATOM 38 HB2 NRQ 1 3.217 -2.499 -0.639 0.149000 HA
ATOM 39 HA31NRQ 1 -2.732 -1.256 -1.058 0.104700 H1
ATOM 40 HA32NRQ 1 -2.089 -2.912 -1.169 0.104700 H1
ATOM 41 HXT NRQ 1 -4.125 -2.951 1.881 0.452000 HO
BOND 1 1 6 2 N1 CA1
BOND 2 1 25 1 N1 H2
BOND 3 2 3 1 CE SD
BOND 4 2 26 1 CE HE1A
BOND 5 2 27 1 CE HE2A
BOND 6 2 28 1 CE HE3
BOND 7 3 4 1 SD CG1
BOND 8 4 5 1 CG1 CB1
BOND 9 4 29 1 CG1 HG11
BOND 10 4 30 1 CG1 HG12
BOND 11 5 6 1 CB1 CA1
BOND 12 5 31 1 CB1 HB11
BOND 13 5 32 1 CB1 HB12
BOND 14 6 7 1 CA1 C1
BOND 15 7 8 2 C1 N2
BOND 16 7 20 1 C1 N3
BOND 17 8 17 1 N2 CA2
BOND 18 9 12 1 OH CZ
BOND 19 9 33 1 OH HOH
BOND 20 10 11 7 CD2 CE2
BOND 21 10 15 8 CD2 CG2
BOND 22 10 34 1 CD2 HD2
BOND 23 11 12 8 CE2 CZ
BOND 24 11 35 1 CE2 HE2
BOND 25 12 13 7 CZ CE1
BOND 26 13 14 8 CE1 CD1
BOND 27 13 36 1 CE1 HE1
BOND 28 14 15 7 CD1 CG2
BOND 29 14 37 1 CD1 HD1
BOND 30 15 16 1 CG2 CB2
BOND 31 16 17 2 CB2 CA2
BOND 32 16 38 1 CB2 HB2
BOND 33 17 18 1 CA2 C2
BOND 34 18 19 2 C2 O2
BOND 35 18 20 1 C2 N3
BOND 36 20 21 1 N3 CA3
BOND 37 21 22 1 CA3 C3
BOND 38 21 39 1 CA3 HA31
BOND 39 21 40 1 CA3 HA32
BOND 40 22 23 2 C3 O3
BOND 41 22 24 1 C3 OXT
BOND 42 24 41 1 OXT HXT
It was advised for me to use the xFPchromophores.lib, and it seems to be
working. I just substituted the NRQ chromophore for the mCherry=CH6. I
minimized the structure with no flaws, but heating will provide better
evaluation if it worked.
Although, I really would love to know what I was missing with PREPGEN.
Thank you.
Message: 6
Date: Mon, 21 Nov 2016 09:11:38 -0500
From: David A Case <david.case.rutgers.edu>
Subject: Re: [AMBER] TUTORIAL B5: Simulating the Green Fluorescent
Protein -PREPGEN Error
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20161121141138.GE88784.scarletmail.rutgers.edu>
Content-Type: text/plain; charset=us-ascii
Can you post the NRQ.ac file so that we could try to reproduce the problem?
...thanks...dac
Message: 5
Date: Sun, 20 Nov 2016 09:31:59 -0500
From: Brent Krueger <kruegerb.hope.edu>
Subject: Re: [AMBER] TUTORIAL B5: Simulating the Green Fluorescent
Protein -PREPGEN Error
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAPjhn9cAp2uAPMeYPwB9DifE9dZfYbM_gir7X61Mbm2Cvd-F0w.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Miles,
I'm afraid I can't help you with these prepgen issues, but I would like to
point out that AMBER now has built-in parameters for a number of
fluorescent protein chromophores. These include EGFP with the CRO
chromophore (and several other fluorescent proteins) that have Tyr and Gly
as the 2nd and 3rd residues and also EBFP with the CR2 chromophore, which
has Ser as the 1st residue. In AmberTools16 you can find the atoms types
for all of these in the xFPchromophores.lib file and modified force field
parameters in frcmod.xFPchromophores file. There is also a leaprc file
that loads these files and sets up some atom types.
The parameters for these xFPs were developed to be modular, so you may be
able to use these atoms types and the frcmod file directly in your
situation. The parameters are meant to work with ff14SB, but they utilize
some atom types from GAFF, which is why the leaprc file needs to do a
little bit more than just load the lib and frcmod files. You will need to
calculate charges for the atoms as these are unique for every situation.
Again, sorry I can't help with prepgen, but if you want any assistance with
atom types, etc. feel free to send me a note directly (off the amber
mailing list).
Cheers,
Brent
On Sat, Nov 19, 2016, Taylor, Miles wrote:
>
> prepgen -i NRQ.ac -o NRQ.prepin -m NRQ.mc -rn NRQ
>
> Also, here is the NRQ.mc file that I created:
>
> HEAD_NAME N1
> TAIL_NAME C3
> MAIN_CHAIN CA1
> MAIN_CHAIN C1
> MAIN_CHAIN N3
> MAIN_CHAIN CA3
> OMIT_NAME H2
> OMIT_NAME OXT
> OMIT_NAME HXT
> PRE_HEAD_TYPE C
> POST_TAIL_TYPE N
> CHARGE 0.0
>
> Segmentation fault (core dumped)
--
Sincerely,
Miles Taylor
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Received on Mon Nov 21 2016 - 13:00:03 PST
