Please keep replies in the same thread rather than starting new topics (I
only say this because I've screwed up in the other direction, unwittingly
posting new threads in a previous topic).
When I run "prepgen -i NRQ.ac -o NRQ.prepin" I get NRQ.prepin with no seg
faults, although valgrind of that run reveals there is a memory error, an
invalid read, which definitely could cause a seg fault depending on your
compilation. Please post the ./configure options you used when building
Amber, and the exact command you used to run prepgen.
Thanks,
Dave
On Mon, Nov 21, 2016 at 3:36 PM, Taylor, Miles <taylormi.oregonstate.edu>
wrote:
> 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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> AMBER.ambermd.org
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>
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Received on Mon Nov 21 2016 - 13:30:02 PST
