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?
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
But MCPB does not seem to understand ".CA.".
Any suggestions?
Thank you
Fabrício
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
>>>>
>>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Apr 28 2012 - 08:30:03 PDT
