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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Received on Wed Jan 18 2012 - 23:30:02 PST
