Hi Audrey -
What kind of calculation do you want to do on this structure? Just a
minimization or MD? It is really difficult to find the best parameter set
from analogy, but I would guess that it will not make a too big difference
for this structure. Generally, minimization is done to get rid of close
contacts. When I minimize nucleic acids in gas phase, for instance, I will
see some distortions on the planes but they will vanishe in an MD run. The
same thing would probably happen in your case. Also, how do you minimize
the structure? In vacuum or using implicit solvent model? You might want
to try to minimize the structure using one of the implicit solvent models
implemented in AMBER if you did not try already. That might resemble the
real environment more than gas phase.
If the aim of the minimization is to prepare the best coordinates for the
MD simulations, you might want to put some restraints on the structure
(this can be positional and/or NMR distance/angle/torsional restraints).
Another thing - I do not see any parameters defined for the sulphur region
in the frcmod file (resid 1 and 9). After creating the bonds did leap give
any error message for that sulphur bond?
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 Sun, 3 Apr 2011, Melanie wrote:
> Hi Ilyas,Thanks for your helpful advice last time. I did what you suggested: I added the bond between residues 1 and 9, and uploaded the required frmcod file. The bond N3-C was easy to define, but the angles and dihedral parameters
> were a little more difficult to choose from. I made some selections, but after minimization, the bond turned out to be skewed (positioned the wrong way), and obviously therefore physically impossible and invalid. Do you have any
> suggestions as to which ones I should choose from the parm99.dat file as an analogy, or how to calculate these parameters. I have attached the frmcod file.
> Thanks,
> Audrey
>
> On Fri, Mar 18, 2011 at 10:39 PM, Ilyas Yildirim <i-yildirim.northwestern.edu> wrote:
> 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
> >>>> ********
> >>>>
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>>
> >> _______________________________________________
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> >>
> >
> > _______________________________________________
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> >
>
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Received on Mon Apr 04 2011 - 07:30:10 PDT
