Re: [AMBER] Missing Parameters

From: Ilyas Yildirim <i-yildirim.northwestern.edu>
Date: Thu, 17 Mar 2011 14:59:00 -0500 (CDT)

Melanie -

I tested both structures and leap could create the prmtop/inpcrd files.
There are close contact problems printed out in leap, which you can
disregard. Those close contact problems can be solved after doing
minimization on the structure.

I would not directly use a .pdb file downloaded from pdb.org. I would
first post-process it before loading it to leap. In your case, for some
reason which I dont know, leap does not understand the structure. Look at
the attached tmp.pdb file, which is the processed version of 3NJW pdb
file. Using this .pdb will create prmtop/inpcrd.

Also, do you need water molecules from the .pdb file? If not, remove them
before creating the prmtop/inpcrd files.

Good luck,

   Ilyas Yildirim, Ph.D.
   -----------------------------------------------------------
   = Department of Chemistry - 2145 Sheridan Road =
   = Northwestern University - Evanston, IL 60208 =
   = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
   = http://www.pas.rochester.edu/~yildirim/ =
   -----------------------------------------------------------


On Thu, 17 Mar 2011, Melanie wrote:

> Hi Ilyas,
> This should be a regular system. I am using a structure from the PDB; I have
> attached it. As a background, I edited 3NJW_old to 3NJW by changing the CYS
> to CYX, since the structure contains a cysteine disulfide bond. This edit
> fixed some of the original errors I had regarding that particular bond.
> If I were to treat this as a regular system, how would I change the
> structure? And if I have to define my own residue library, would I be using
> the addPdbResMap function or something else?
>
> Thanks very much,
> Melanie
>
> On Tue, Mar 15, 2011 at 11:18 AM, Ilyas Yildirim <
> i-yildirim.northwestern.edu> wrote:
>
>> Melanie - It seems that you have a system where you have a bond (in the
>> atom type notation) N3-C. I checked out parm99.dat and there is not any
>> such bond defined. As a result, you need to defined those missing
>> parameters. Is this a regular system or do you have your own residue
>> library defined, which you want to use in this particular system?
>>
>> Ilyas Yildirim, Ph.D.
>> -----------------------------------------------------------
>> = Department of Chemistry - 2145 Sheridan Road =
>> = Northwestern University - Evanston, IL 60208 =
>> = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
>> = http://www.pas.rochester.edu/~yildirim/ =
>> -----------------------------------------------------------
>>
>>
>> On Tue, 15 Mar 2011, Melanie wrote:
>>
>>> Hi all,
>>> I've been trying to figure out what is wrong with my molecule. This set
>> of
>>> missing parameters appears to be stemming from one particular bond or
>> area.
>>> When leap would not save my parameter files because of these errors, I
>> tried
>>> to figure out which parameters I was missing by using parmchk and
>>> antechamber; unfortunately, both of these also ended with an error
>> message.
>>> I also tried addIons, to no avail. Can someone please tell me how to fix
>>> this, and also *how to detect certain basic errors that may cause a
>>> parameter file to not be saved*, etc.
>>> I have pasted the missing parameters error and antechamber errors below,
>> as
>>> well as attached the leap.log file.
>>>
>>> *> saveamberparm njw njw.prmtop njw.inpcrd*
>>> *Checking Unit.*
>>> *WARNING: The unperturbed charge of the unit: -1.000000 is not zero.*
>>> *
>>> *
>>> * -- ignoring the warning.*
>>> *
>>> *
>>> *Building topology.*
>>> *Building atom parameters.*
>>> *Building bond parameters.*
>>> *Could not find bond parameter for: N3 - C*
>>> *Building angle parameters.*
>>> *Could not find angle parameter: CT - N3 - C*
>>> *Could not find angle parameter: H - N3 - C*
>>> *Could not find angle parameter: H - N3 - C*
>>> *Could not find angle parameter: H - N3 - C*
>>> *Could not find angle parameter: N3 - C - CT*
>>> *Could not find angle parameter: N3 - C - O2*
>>> *Could not find angle parameter: N3 - C - O2*
>>> *Building proper torsion parameters.*
>>> * ** No torsion terms for CT-N3-C-CT*
>>> * ** No torsion terms for CT-N3-C-O2*
>>> * ** No torsion terms for CT-N3-C-O2*
>>> * ** No torsion terms for H-N3-C-CT*
>>> * ** No torsion terms for H-N3-C-O2*
>>> * ** No torsion terms for H-N3-C-O2*
>>> * ** No torsion terms for H-N3-C-CT*
>>> * ** No torsion terms for H-N3-C-O2*
>>> * ** No torsion terms for H-N3-C-O2*
>>> * ** No torsion terms for H-N3-C-CT*
>>> * ** No torsion terms for H-N3-C-O2*
>>> * ** No torsion terms for H-N3-C-O2*
>>> *Building improper torsion parameters.*
>>> * ** Warning: No sp2 improper torsion term for C*-CN-CB-CA*
>>> * atoms are: CG CE2 CD2 CE3*
>>> * ** Warning: No sp2 improper torsion term for NA-CA-CN-CB*
>>> * atoms are: NE1 CZ2 CE2 CD2*
>>> * ** Warning: No sp2 improper torsion term for CT-O2-C-N3*
>>> * atoms are: CB OD1 CG N*
>>> * ** Warning: No sp2 improper torsion term for CT-O2-C-N3*
>>> * atoms are: CB OD2 CG N*
>>> * ** Warning: No sp2 improper torsion term for C*-CN-CB-CA*
>>> * atoms are: CG CE2 CD2 CE3*
>>> * ** Warning: No sp2 improper torsion term for NA-CA-CN-CB*
>>> * atoms are: NE1 CZ2 CE2 CD2*
>>> * ** Warning: No sp2 improper torsion term for C*-CN-CB-CA*
>>> * atoms are: CG CE2 CD2 CE3*
>>> * ** Warning: No sp2 improper torsion term for NA-CA-CN-CB*
>>> * atoms are: NE1 CZ2 CE2 CD2*
>>> * total 62 improper torsions applied*
>>> *Building H-Bond parameters.*
>>> *Parameter file was not saved.*
>>>
>>> --------------------------
>>>
>>> *[.login2 ~]$ $AMBERHOME/exe/antechamber -i
>> /u/home/campus/template/3NJW.pdb
>>> -fi pdb -o njw.prepin -fo prepi -c bcc -s 2*
>>> *Running: /u/home2/ppk/amber10/bin/bondtype -j full -i
>>> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac*
>>> *sh: /u/home2/ppk/amber10/bin/bondtype: Permission denied*
>>> *Error: cannot run "/u/home2/ppk/amber10/bin/bondtype -j full -i
>>> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
>>> judgebondtype() of antechamber.c properly, exit*
>>>
>>>
>>>
>>> Thank you,
>>> Melanie
>>>
>>
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>
>
>
> --
> ********
> Minnie
> ********
>

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Received on Thu Mar 17 2011 - 13:00:04 PDT
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