Dear Chris,
Once the new Cartesian coordinates are printed in the console you can
use the left/middle buttons of your mouse to select/copy these
Cartesian coordinates in a new text editor window (kate & geany allow
mode block selection). Then, you can modify the atom order/atom names
and save the new PDB file using the text editor of your choice...
regards, Francois
> I am having trouble with adding the hydrogens to the structure. I have the
> jmol application and I have added the hydrogens, and have written in the
> console "write coord pdb", but how do I save this information to something
> I can edit. Supposedly java applets won't allow simple cut/copy/paste, so
> how do you recommend getting my pdb coordinates onto an editable space. In
> the tutorial, it just says save the coords, but it seems I must be missing
> something simple.
> On Thu, Jan 19, 2012 at 9:35 AM, Chris Bryant <csb61.case.edu> wrote:
>
>> 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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Received on Tue Jan 24 2012 - 03:30:02 PST
