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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Received on Thu Jan 19 2012 - 01:00:02 PST
