Dear Chris,
> Well, the problem is that I cannot copy the cartesian coordinates; no
> option pops up to copy the coords when I highlight them and right click. I
> cannot drag them over to an editor either. I have also tried right
> clicking on the molecule visualizer (where the molecule structure appears)
> and I get the menu that gives me the options to Select, View, Molecule Kit,
> etc.... and the bottom option, About -> Filename-out -> Filename.pdb view,
> which normally opens up a page with the coords in a copy-able format, does
> not open up this page if I have altered the molecule, like adding
> hydrogens. Instead of giving me the coords, it sends me to this page:
> http://q4md-forcefieldtools.org/REDS/error-notfound.php
>
> Any additional help on this problem would be greatly appreciated.
I look at your job P5956: hydrogens were added
P5951: hydrogens are missing
http://q4md-forcefieldtools.org/REDS/faq.php#19
- create hydrogens in the Java applet (then modify the structure)
then right click -> Display (below Console) and you can display many
pieces of information. Jmol is powerful; but you need to understand
how it works.
Another approach is to use the XLEaP program to add hydrogens. Once
again, you have to spend time to learn how it works..
--
I look at your modified residue and the side chain is large and
contains several charged groups... You might consider splitting this
side chain into different building blocks otherwise the conformation
you will get geometry optimization might not be representative...
regards, Francois
> On Tue, Jan 24, 2012 at 6:08 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
>> 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<http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#ATOM-NAME>
>>>>> & more generally:
>>>>>
>>>>> http://q4md-forcefieldtools.**org/Tutorial/Tutorial-1.php#**Fig1<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<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<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>
>>>>> >>>> &
>>>>> http://q4md-forcefieldtools.**org/Tutorial/Tutorial-3.php#24<http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24>
>>>>> >>>> & even http://q4md-forcefieldtools.**
>>>>> org/Tutorial/Tutorial-3.php#25<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 <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<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?
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Received on Tue Jan 31 2012 - 00:00:02 PST
