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?
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> 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 Wed Jan 18 2012 - 11:30:03 PST
