On Sat, Apr 28, 2012 at 8:33 PM, Fabrício Bracht <bracht.iq.ufrj.br> wrote:
> Hello. I am sorry to send this email again, but it seems we had some
> problem with the email server here and, just to be sure, I am
> resending the message. I am still having some problems with the
> addFragment line. I have tried a number of different ways, but since I
> am not entirely sure of what ddo the bd, ag and tr variables mean, I
> don´t know if I can use them properly. For cysteine, I have now
> specified:
>
> addFragment terminal/CH3 bd /NAME/CLR/CY2-2/.CB. ag
> /NAME/CLR/HD2-2/.HB2 tr /NAME/CLR/CY2-2/.SG. 89.0
>
> for one cysteine residue and:
>
> addFragment terminal/CH3 bd /NAME/CLR/CY1-3/.CB. ag
> /NAME/CLR/HD1-3/.HB2 tr /NAME/CLR/CY1-3/.SG. 31.0
>
> and strangely enough, one of the cysteine residues comes out alright
> with a CH3 attached to the beta carbon, but the other one doesn´t.
> Cysteine 31 comes out with a "flying" CH3 (not attached to anything).
>
> Any help here would be appreciated.
> Thank you
> Fabrício
>
> Please ignore the last email. I've solved the problem. Turns out I was
> using the wrong pdb file as input.
> I have just one other question. I've changed the addfragment part, but
> I'm not quite sure I understood the syntax. What does bd and tr mean?
>
bd means bond distance, ag means angle while tr means torsion. Generally bd
and ag's are not define as they pick up the default val;ues. Trs should
always be mentioned based on your structure.
> I've written the lines like this:
> addFragment terminal/CH3 bd /NAME/CLR/CY2-2/.CA. ag
> /NAME/CLR/HD1-1/.CB. tr /NAME/CLR/CY2-2/.SG. 89.0
>
> The above line has a syntax mistake. U want to add CH3 to CY2-2, and you
mention HD1-1 as the residue name for angle.
> But MCPB does not seem to understand ".CA.".
> Any suggestions?
> Thank you
> Fabrício
>
> Hope this helps.
>
Ashwini
>
> Em 26 de abril de 2012 11:00, Fabrício Bracht <bracht.iq.ufrj.br>
> escreveu:
> > Hello. It is named MOH in my pdb file. I've have three chain labels in
> > my original pdb file. The first (A) is the protein, the second (B) is
> > the ZN atom and the third (C) is the MOH hydroxil residue. I have
> > filled the blank with every single number I could think of
> > (1,2,3,4,5,.....etc) but the error comes out always the same way:
> > ### ### ### ###
> > ### MTK++ Info ###
> > ### Function: selection::parse ###
> > ### Message: selection string = /1AMP_OH/CLR/OH1
> > ### ### ### ###
> >
> > ### ### ### ###
> > ### MTK++ Info ###
> > ### Function: selection::parse ###
> > ### Message: selection string = /1AMP_OH/3/MOH-171
> > ### ### ### ###
> >
> > ### ### ### ###
> > ### MTK++ Error ###
> > ### Function: selection::parse ###
> > ### Message: Can't find: MOH-171 in molecule: MOH /col/mol/smol
> > selection error (4)
> > ### ### ### ###
> >
> > ### ### ### ###
> > ### MTK++ Error ###
> > ### Function: MCPB::addToResidue ###
> >
> > I then changed in the script the line that designated the MOH residue.
> > It turned out like this:
> >
> > # Create OH1-5 from MOH-171
> > createResidue OH1 in CLR
> > addToResidue /NAME/CLR/OH1 /NAME/3/MOH-171/MOH
> >
> > This way, the error comes out like this:
> >
> > ### ### ### ###
> > ### MTK++ Info ###
> > ### Function: selection::parse ###
> > ### Message: selection string = /1AMP_OH/CLR/OH1
> > ### ### ### ###
> >
> > ### ### ### ###
> > ### MTK++ Info ###
> > ### Function: selection::parse ###
> > ### Message: selection string = /1AMP_OH/3/MOH-171/MOH
> > ### ### ### ###
> >
> > ### ### ### ###
> > ### MTK++ Error ###
> > ### Function: selection::parse ###
> > ### Message: /col/mol/smol/atom selection error (6) ... exiting
> > ### ### ### ###
> >
> > ### ### ### ###
> > ### MTK++ Error ###
> > ### Function: MCPB::addToResidue ###
> > ### Message: Error in selection parsing
> > ### ### ### ###
> >
> > Any suggestions?
> > Thank you
> > Fabricio
> >
> > Em 25 de abril de 2012 22:14, Yang, Yue <yang.qtp.gmail.com> escreveu:
> >>
> >> Hard to tell. Is it MOH or HOH in your PDB? Besides, why do you leave
> it blank at /NAME/_/MOH-171? It should be 'Chain' number - anything other
> than protein should be count as 1 chain. Thus if you have a single chain
> for your protein which has 170 residues, you should put 2 there; if you
> have double chains in your protein which has 170 residues, you should put 3
> there; if you have a single chain in your protein which has 168 residues
> and residue #169 and #170 are water, you should put 4 there...
> >>
> >> Good luck,
> >> Yue
> >>
> >> On Apr 25, 2012, at 6:39 AM, Fabrício Bracht wrote:
> >>
> >>> Thank you Yue for the reply.
> >>> I have changed ".SG" to ".SG.", and this problem seems solved. I have
> >>> had, however, another problem. Now MCPB gives a segmentation fault
> >>> without any other error message. Apparently the program terminates
> >>> when it is processing the lines:
> >>>
> >>> # Create OH1-5 from HOH-171
> >>> createResidue OH1 in CLR
> >>> addToResidue /NAME/CLR/OH1 /NAME//MOH-171
> >>>
> >>> Any suggestions?
> >>> Thank you
> >>> Fabrício
> >>>
> >>>
> >>> Em 23 de abril de 2012 20:31, Yang, Yue <yang.qtp.gmail.com> escreveu:
> >>>>
> >>>> Try .SG. instead of .SG. The former is of size 4 while the latter
> (which caused
> >>>> the error) is of size 3.
> >>>>
> >>>> Yue
> >>>>
> >>>> On Apr 23, 2012, at 8:21 AM, Fabrício Bracht wrote:
> >>>>
> >>>>> Hi there. I am trying to create parameters in order to simulate an
> >>>>> enzime with 2CYS residues and a histidine residue bound to Zn atom in
> >>>>> the active site. I am using amber12 and MCPB to do this. I am
> >>>>> basically using the same scripts given by the MTK++ manual (MCPB
> >>>>> section) and trying to adapt them to my reality. When performing the
> >>>>> NAME_sidechain.bcl part, I've noticed that there is this section with
> >>>>> "copyStdResidue", "copyAtomType", and "setAtomType" that I assume are
> >>>>> getting the atom names and residue names from the forcefield database
> >>>>> and simply redirecting them to the MCPB routine, right? In the
> >>>>> original file, there is a section saying "# Create new atom types",
> >>>>> but these new atom types are not used anywhere else in the script.
> >>>>> Regarding my system, I have not found the correct way to deal with
> the
> >>>>> SG atom in CYM residue. I've read in another post that the correct
> >>>>> atom name for parm94 is actually SH (and not SG). So I've created a
> >>>>> section in the script that goes like this:
> >>>>>
> >>>>> copyAtomType parm94/SH NAME/SH
> >>>>>
> >>>>> setAtomType NAME/CY2/.SG NAME/SH
> >>>>>
> >>>>> This is for one of my cysteine residues, named later on CY2 by the
> lines:
> >>>>> # Create CY2-2 from CYM-89
> >>>>> createResidue CY2 in CLR
> >>>>> addToResidue /NAME/CLR/CY2 /NAME/1/CYM-89 not bb
> >>>>>
> >>>>> When i run MCPB with this script I get an error in the log saying
> >>>>>
> >>>>> ### ### ### ###
> >>>>> ### MTK++ Error ###
> >>>>> ### Function: MCPB::setAtomType ###
> >>>>> ### Message: Error in setAtomType -> atom name must be of size 4
> ... exiting
> >>>>> ### ### ### ###
> >>>>>
> >>>>> I'm kinda lost here. Wonder if you could give me a help.
> >>>>>
> >>>>> Thanks
> >>>>> Fabrício
> >>>>>
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>
>
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Received on Sat Apr 28 2012 - 22:30:02 PDT
