Melanie - I have a question regarding the .pdb file you are trying to
analyze: Are there any covalent bonds between resid 1 and 9, and resid 6
and 19 in this structure? If yes, then you need to create bonds between
those atoms using the 'bond' command in leap. I think that was the problem
you first encountered, is that right? In such a case, the force field
might not have necessary parameters to create the prmtop/inpcrd files.
Something was weird about this structure when I looked at it in VMD but
did not see it at first. It seems that this is not a regular protein;
there are covalent bonds between different residues. As a result you see
those errors in leap. For instance, there is no N3-C bond defined in the
force field but because of these non-regular covalent bonds, leap looks
for this bond and cannot find it. You need to create an frcmod file and
define those missing bond/angle/torsion parameters for N3-C and SH-S. You
can make analogy with the other types (For SH-S and N3-C, you might be
able to use S-S and N-C paramaters).
The .pdb file I attached in my previous email does not have these extra
covalent bonds defined; so it will not be useful. Hope this helps.
Best regards,
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 Fri, 18 Mar 2011, Ilyas Yildirim wrote:
> On Fri, 18 Mar 2011, Melanie wrote:
>
>> Thank you both very much for your help. One last question: Ilyas, what did
>> you use to process the .pdb file? Did you also use the H++ program (
>> http://biophysics.cs.vt.edu/H++/ ) Marek used?
>
> I am not familiar with that program. I just used a one line command in
> linux to process the file. Maybe the program you refer to might be used as
> well but I do not know.
>
> One mistake I saw in people is that they disregard some important messages
> leap gives. Sometimes, when an original .pdb file is used to create the
> prmtop/inpcrd files, leap will add some extra heavy atoms and create the
> files accordingly. This happens when the naming of the atom is not
> recognized by leap. My rule of thumb is to play with the .pdb file until
> leap does not give any critical error messages (or weird messages like
> creating a new atom). In your .pdb file, I just kept the lines starting
> with ATOM, put TER cards when a sequence/strand is finished, and removed
> the water molecules. I would suggest you to do the same.
>
> Best regards,
>
>>
>> On Thu, Mar 17, 2011 at 12:59 PM, Ilyas Yildirim <
>> i-yildirim.northwestern.edu> wrote:
>>
>>> 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
>>>>>>
>>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> ********
>>>> Minnie
>>>> ********
>>>>
>>>
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>>>
>>>
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Received on Fri Mar 18 2011 - 23:00:03 PDT
