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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Received on Wed Jan 18 2012 - 22:30:02 PST
