Thank you so much for the feedback!
On Thu, Jan 19, 2012 at 3:50 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Chris,
>
> When you have a problem always report the 'PXXXX' R.E.D. Server job so
> that we can easily track the problem...
>
> in your P2N file, you have also errors; for instance:
> ATOM 23 NA23 SEB 1 -8.660 -0.810 -0.780
> NAV
>
> -> here this a Na atom and not a N atom
>
> if you use Ante_R.E.D. 2.0 it is easy to follow as an additional
> column with the chemical symbol is added in the P2N file for
> information:
>
> ATOM 23 NA23 SEB 1 -8.660 -0.810 -0.780 NAV Na
>
> You should have:
> ATOM 23 N23 SEB 1 -8.660 -0.810 -0.780 NAV Na
>
> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#ATOM-NAME
> & more generally:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#Fig1
>
> regards, Francois
>
>
> Quoting FyD <fyd.q4md-forcefieldtools.org>:
>
> > Chris,
> >
> > I just updated the tutorial to underline your problem...
> >
> > Moreover, in your case use Ante_R.E.D. 2.0 to generate the P2N file
> > for the dipeptide. It looks like you used Ante_R.E.D. 1.x and then it
> > was manually modified... (This type of modification lead often to
> > problems: the atom order is not anymore in agreement with the atom
> > connectivities...)
> >
> > regards, Francois
> >
> >
> > Quoting FyD <fyd.q4md-forcefieldtools.org>:
> >
> >> Dear Chris,
> >>
> >> all should be in the tutorial:
> >> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
> >>
> >> & the hydrogens in your structure should be present...
> >> See http://q4md-forcefieldtools.org/REDS/faq.php#19 to add hydrogens
> >> to your structure
> >>
> >> regards, Francois
> >>
> >>
> >>> I successfully added the caps, however, when I try and complete the
> >>> tutorial from #25, the job ends quickly and I get an error message:
> >>>
> >>> Automatic generation of molecular fragments by R.E.D. Server.
> >>>
> >>> The connectivity carbon C(ACE)-nitrogen N(AA) cannot be found
> >>> The connectivity nitrogen CO(AA)-oxygen OC(AA) cannot be found
> >>>
> >>> R.E.D. IV job stopped because of a problem in the P2N file you
> uploaded.
> >>>
> >>> The p2n file I am using is:
> >>>
> >>> REMARK
> >>> REMARK TITLE SEBCAPPED
> >>> REMARK CHARGE-VALUE 0
> >>> REMARK MULTIPLICITY-VALUE 1
> >>> REMARK
> >>> ATOM 1 C1 ACE 1 -9.420 6.810 -4.210
> >>> CAZ
> >>> ATOM 2 O2 ACE 1 -8.440 6.940 -4.940
> >>> OAD
> >>> ATOM 3 C3 ACE 1 -9.980 7.990 -3.430
> >>> CAB
> >>> ATOM 33 N33 SEB 2 -10.110 5.660 -4.070
> N
> >>> ATOM 4 O4 SEB 2 -11.750 2.280 -5.880
> >>> OAE
> >>> ATOM 5 C5 SEB 2 -11.040 1.310 -5.510
> >>> CBA
> >>> ATOM 6 O6 SEB 2 -10.460 1.230 -4.400
> >>> OAL
> >>> ATOM 7 C7 SEB 2 -10.860 0.160 -6.500
> >>> CAQ
> >>> ATOM 8 C8 SEB 2 -9.630 0.370 -7.390
> >>> CAP
> >>> ATOM 9 C9 SEB 2 -8.300 0.260 -6.640
> >>> CAR
> >>> ATOM 10 C10 SEB 2 -8.070 -1.140 -6.060
> >>> CBD
> >>> ATOM 11 O11 SEB 2 -8.410 -2.150 -6.680
> >>> OAH
> >>> ATOM 12 O12 SEB 2 -7.410 -1.140 -4.870
> >>> OAY
> >>> ATOM 13 C13 SEB 2 -7.420 -2.380 -4.140
> >>> CAT
> >>> ATOM 14 C14 SEB 2 -7.430 -2.130 -2.620
> >>> CBI
> >>> ATOM 15 C15 SEB 2 -6.070 -1.520 -2.230
> >>> CAC
> >>> ATOM 16 S16 SEB 2 -7.620 -3.840 -1.730
> >>> SBH
> >>> ATOM 17 O17 SEB 2 -6.310 -4.610 -1.880
> >>> OAJ
> >>> ATOM 18 O18 SEB 2 -8.740 -4.620 -2.420
> >>> OAK
> >>> ATOM 19 C19 SEB 2 -8.620 -1.210 -2.210
> >>> CBG
> >>> ATOM 20 C20 SEB 2 -10.000 -1.770 -2.600
> >>> CBB
> >>> ATOM 21 O21 SEB 2 -10.580 -2.510 -1.770
> >>> OAM
> >>> ATOM 22 O22 SEB 2 -10.450 -1.460 -3.720
> >>> OAF
> >>> ATOM 23 N23 SEB 2 -8.660 -0.810 -0.780
> >>> NV
> >>> ATOM 24 C24 SEB 2 -8.110 0.380 -0.550
> >>> CAN
> >>> ATOM 25 C25 SEB 2 -8.810 1.620 -1.130
> >>> CAO
> >>> ATOM 26 C26 SEB 2 -8.230 2.160 -2.440
> >>> CBC
> >>> ATOM 27 O27 SEB 2 -7.450 1.480 -3.110
> >>> OAG
> >>> ATOM 28 O28 SEB 2 -8.680 3.420 -2.760
> >>> OAX
> >>> ATOM 29 C29 SEB 2 -8.420 3.850 -4.100
> >>> CB
> >>> ATOM 30 C30 SEB 2 -9.710 4.380 -4.720
> >>> CA
> >>> ATOM 31 C31 SEB 2 -9.630 4.450 -6.250
> C
> >>> ATOM 32 O32 SEB 2 -8.990 3.580 -6.860
> O
> >>> ATOM 34 N34 NME 3 -10.420 5.370 -6.840
> >>> NU
> >>> ATOM 35 C35 NME 3 -10.400 5.540 -8.300
> >>> CAA
> >>> CONECT 1 2 3 33
> >>> CONECT 2 1
> >>> CONECT 3 1
> >>> CONECT 4 5
> >>> CONECT 5 4 6 7
> >>> CONECT 6 5
> >>> CONECT 7 5 8
> >>> CONECT 8 7 9
> >>> CONECT 9 8 10
> >>> CONECT 10 9 11 12
> >>> CONECT 11 10
> >>> CONECT 12 10 13
> >>> CONECT 13 12 14
> >>> CONECT 14 13 15 16 19
> >>> CONECT 15 14
> >>> CONECT 16 14 17 18
> >>> CONECT 17 16
> >>> CONECT 18 16
> >>> CONECT 19 14 20 23
> >>> CONECT 20 19 21 22
> >>> CONECT 21 20
> >>> CONECT 22 20
> >>> CONECT 23 19 24
> >>> CONECT 24 23 25
> >>> CONECT 25 24 26
> >>> CONECT 26 25 27 28
> >>> CONECT 27 26
> >>> CONECT 28 26 29
> >>> CONECT 29 28 30
> >>> CONECT 30 29 31 33
> >>> CONECT 31 30 32 34
> >>> CONECT 32 31
> >>> CONECT 33 1 30
> >>> CONECT 34 31 35
> >>> CONECT 35 34
> >>> END
> >>>
> >>> Any idea how I can fix my error? All of the atoms seem to connect
> fine, so
> >>> I'm not sure why the error message says the atom connectivity is wrong.
> >>>
> >>> On Sat, Jan 14, 2012 at 2:27 AM, FyD <fyd.q4md-forcefieldtools.org>
> wrote:
> >>>
> >>>> Dear Chris,
> >>>>
> >>>> Did you look at the q4md-fft tutorials?
> >>>> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
> >>>> & http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
> >>>> & even http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
> >>>> (we recently made this procedure even more simple thanks to the help
> >>>> of the R.E.D. Server users...)
> >>>>
> >>>> Now, if you have a big molecule with a peptide bond, and you want to
> >>>> split this molecule into two elementary building blocks by adding the
> >>>> ACE & NME caps, below is the principle; check that peptide bonds are
> >>>> all trans (except if you choose it)
> >>>>
> >>>> O O 2 INTRA-MCC O
> >>>> ...C-N... --> ...C-NME ACE-N... --> ...C N...
> >>>> H H H
> >>>> 2 building blocks 2 fragments to be
> connected
> >>>> in LEaP
> >>>>
> >>>> if something is not clear, do not hesitate to ask more questions...
> >>>>
> >>>> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#Fig1
> >>>> to create prmtop/prmcrd files using Ante_R.E.D./R.E.D./R.E.D. Server
> >>>>
> >>>> regards, Francois
> >>>>
> >>>>
> >>>> > I am trying to use R.E.D.S to build force field libraries for a non
> >>>> > standard serine residue, which is covalently bonded to a drug.
> However,
> >>>> I
> >>>> > am having trouble placing the ACE and NME capping groups. I have
> read
> >>>> > through the this
> >>>> > <http://ambermd.org/tutorials/basic/tutorial1/section2.htm>tutorial
> on
> >>>> > Amber but my problem is 1) I cannot create .prmtop and .inpcrd
> >>>> > files from a non standard residue, and 2) the computing cluster I
> am on
> >>>> > does not support graphical interfacing so I am stuck using only
> tleap,
> >>>> > which this tutorial does not discuss. Could anyone provide me
> methods
> >>>> > which they have used to cap residues with ACE and NME that don't
> involve
> >>>> > the use of xleap or the need to build prmtop and inpcrd files?
> >>
> >> ----- End forwarded message -----
>
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Chris Bryant
Biochemistry B.S.
Philosophy B.A.
Vice President, Alpha Chi Sigma
Case Western Reserve University 2013
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Received on Thu Jan 19 2012 - 07:00:02 PST
