From: Margaret Shun Cheung (mscheung_at_ipst.umd.edu)
Date: Thu Apr 06 2006 - 16:42:41 CDT
Dear Peter,
HALELULYA! It worked! Minimization was sucessful!!!
Sincerely,
Margaret
On Thu, 6 Apr 2006, Peter Freddolino wrote:
> Dear Margaret,
> there appears to be a problem with the charmm topology file, in that
> the CT1 patch does not work properly for glycine residues. I have
> prepared a different patch that should. If you add this to your
> topology file, and then rerun psfgen using CT1G (instead of CT1) as
> your C terminal patch, things should work. Please let me know if you
> still have problems.
> Best,
> Peter
>
>
> PRES CT1G 0.00 ! methylated C-terminus from methyl acetate
> GROUP ! for use with glycine
> ATOM N NH1 -0.47 !
> ATOM HN H 0.31 !
> ATOM CA CT2 0.08 !
> ATOM HA1 HB 0.09 !
> ATOM HA2 HB 0.09 !
> ATOM C CD 0.63 !
> ATOM OT1 OB -0.52 !
> ATOM OT2 OS -0.34 !
> ATOM CT CT3 -0.14 !
> ATOM HT1 HA 0.09 !
> ATOM HT2 HA 0.09 !
> ATOM HT3 HA 0.09 !
> DELETE ATOM O
> BOND C OT2 OT2 CT
> BOND CT HT1 CT HT2 CT HT3
> DOUBLE C OT1
> IMPR C CA OT2 OT1
> ACCEPTOR OT1 C
> ACCEPTOR OT2 C
> IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000
> IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000
> IC CA C OT2 CT 0.0000 0.0000 180.0000 0.0000 0.0000
> IC C OT2 CT HT1 0.0000 0.0000 0.0000 0.0000 0.0000
> IC C OT2 CT HT2 0.0000 0.0000 120.0000 0.0000 0.0000
> IC C OT2 CT HT3 0.0000 0.0000 240.0000 0.0000 0.0000
>
>
>
> Margaret Shun Cheung wrote:
>
>> Dear Peter,
>> Thank you for the email. My last entry of the PDB file (I guess it's
>> the
>> C terminus) is a Gly.
>> (I noticed from the archive that Gly at N-terminus
>> will be automatically patched with GLYP. I didn't get any info for
>> Gly
>> at the C-terminus.)
>> I don't have prolines. Thank you very much for your help and your
>> patience for newbie questions!
>> Sincerely,
>> Margaret
>>
>>
>> On Thu, 6 Apr 2006, Peter Freddolino wrote:
>>
>>> Hi Margaret,
>>> this is odd, actually; normally you shouldn't have an angle of the
>>> type you're describing. Is your N or C terminal residue a proline
>>> or glycine? If not, could you please send me your psf and pdb?
>>> Peter
>>>
>>> Margaret Shun Cheung wrote:
>>>
>>>>
>>>> Dear VMD and NAMD users,
>>>> Sorry for this lengthy email. I was advised to spread this email
>>>> list
>>>> to NAMD-L about parameter for CT1, a methylated C-term).
>>>> I followed procedures to include a methylated C-term using psfgen
>>>> ({auto angles dihedrals}).
>>>> But when I minimize it using "par_all27_prot_lipid.inp", then
>>>> NAMD generates a FATAL error in (2).
>>>>
>>>> Did I miss something in my psfgen or namd parameters?
>>>> Thank you.
>>>> Sincerely,
>>>> Margaret
>>>>
>>>>
>>>>
>>>> On Thu, 6 Apr 2006, Peter Freddolino wrote:
>>>>
>>>>> Hi Margaret,
>>>>> what parameter file are you using? The error you get (2)
>>>>> indicates that you don't have parameters for some piece of what
>>>>> you're simulating (likely one of the nonstandard terminii).
>>>>> Please let us know. You may also want to move the discussion to
>>>>> NAMDL if you have further questions about this.
>>>>> Best,
>>>>> Peter
>>>>>
>>>>> Margaret Shun Cheung wrote:
>>>>>
>>>>>>
>>>>>> Dear All,
>>>>>> Just a quick followup on what I tried with "auto none" as I
>>>>>> searched on the web. After I included it and generated a new psf
>>>>>> file, I got rid of the FATAL ERROR, but the minimization process
>>>>>> was completely screwed up.
>>>>>> Is there another way to get around with it? Thank you.
>>>>>> Sincerely,
>>>>>> Margaret
>>>>>>
>>>>>> On Thu, 6 Apr 2006, Margaret Shun Cheung wrote:
>>>>>>
>>>>>>> Dear All,
>>>>>>>
>>>>>>> I tried it with psfgen using the syntax in (1). But when I
>>>>>>> tried to minimize the structure, namd gave me another error in
>>>>>>> (2).
>>>>>>> Do I miss something in the psfgen input file? Thank you!
>>>>>>> Sincerely,
>>>>>>> Margaret
>>>>>>>
>>>>>>> (1)
>>>>>>> segment A {
>>>>>>> pdb my.pdb
>>>>>>> first ACE
>>>>>>> last CT1
>>>>>>> }
>>>>>>>
>>>>>>>
>>>>>>> (2)
>>>>>>> ------------- Processor 0 Exiting: Called CmiAbort ------------
>>>>>>> Reason: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HB CT1
>>>>>>> HB
>>>>>>>
>>>>>>> Charm++ fatal error:
>>>>>>> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HB CT1 HB
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Thu, 6 Apr 2006, Margaret Shun Cheung wrote:
>>>>>>>
>>>>>>>>
>>>>>>>> Dear All,
>>>>>>>> Thank you very much for the tips!
>>>>>>>> Sincerely,
>>>>>>>> Margaret
>>>>>>>>
>>>>>>>> On Thu, 6 Apr 2006, Peter Freddolino wrote:
>>>>>>>>
>>>>>>>>> Dear Margaret,
>>>>>>>>> you may want to look at some of the other patches that Marcos
>>>>>>>>> mentioned in his email, such as ACE (acetylated N terminus)
>>>>>>>>> or CT1 (methylated C terminus). They are all present in the
>>>>>>>>> topology file.
>>>>>>>>> Best,
>>>>>>>>> Peter
>>>>>>>>>
>>>>>>>>> Margaret Shun Cheung wrote:
>>>>>>>>>
>>>>>>>>>> Dear John and Marcos,
>>>>>>>>>>
>>>>>>>>>> Thank you for the email. I looked up definitions for NTER
>>>>>>>>>> and CTER
>>>>>>>>>> and their chemical structures; this is probably not what I'd
>>>>>>>>>> expect
>>>>>>>>>> in my simulations.
>>>>>>>>>> I wonder if there are options for "capped" termini, ie
>>>>>>>>>> Acetyl and N-methyl options, such that charges at termini
>>>>>>>>>> are neutral. Or is there another way to get around
>>>>>>>>>> with charges at ends, please drop a hint.
>>>>>>>>>>
>>>>>>>>>> Thank you!
>>>>>>>>>> Sincerely,
>>>>>>>>>> Margaret
>>>>>>>>>>
>>>>>>>>>> On Thu, 6 Apr 2006, Marcos Sotomayor wrote:
>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Hi Margaret,
>>>>>>>>>>>
>>>>>>>>>>> psfgen will build segments of your protein using a topology
>>>>>>>>>>> file which defines different residues and patches. The
>>>>>>>>>>> usual CHARMM topology file assumes standard protonation
>>>>>>>>>>> states for residues labeled ASP (-), GLU (-), ARG (+), and
>>>>>>>>>>> LYS (+). There are three options for histidine and you need
>>>>>>>>>>> to choose one of them (HSE, HSD or HSP, you may want to see
>>>>>>>>>>> the first chapter of the NAMD tutorial). There are several
>>>>>>>>>>> options for the termini too (charged and uncharged, etc.),
>>>>>>>>>>> which can be selected through patches (which can also be
>>>>>>>>>>> used to protonate ASP and GLU, see the patches PRES ACP,
>>>>>>>>>>> CTER, CT1, ASPP and GLUP in the CHARMM topology file
>>>>>>>>>>> provided by VMD).
>>>>>>>>>>>
>>>>>>>>>>> hope that helps!
>>>>>>>>>>> Marcos
>>>>>>>>>>>
>>>>>>>>>>> On Wed, 5 Apr 2006, John Stone wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi,
>>>>>>>>>>>> You'll want to read through the NAMD tutorial section
>>>>>>>>>>>> about topology files, as it describes the purpose of
>>>>>>>>>>>> patches
>>>>>>>>>>>> for the the terminal residues:
>>>>>>>>>>>> http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-html/node21.html
>>>>>>>>>>>> I don't know the answer regarding charged states, you'll
>>>>>>>>>>>> have to ask
>>>>>>>>>>>> Jim Phillips about that, (jim_at_ks.uiuc.edu) as he wrote the
>>>>>>>>>>>> psfgen.
>>>>>>>>>>>>
>>>>>>>>>>>> John Stone
>>>>>>>>>>>> vmd_at_ks.uiuc.edu
>>>>>>>>>>>>
>>>>>>>>>>>> On Tue, Apr 04, 2006 at 05:23:25PM -0400, Margaret Shun
>>>>>>>>>>>> Cheung wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Dear VMD wizards,
>>>>>>>>>>>>>
>>>>>>>>>>>>> I would like to know what kind of charged states psfgen
>>>>>>>>>>>>> would generate
>>>>>>>>>>>>> from a standard pdb structure.
>>>>>>>>>>>>> Do I have to worry about adding charges at all?
>>>>>>>>>>>>> Also, when I read the psfgen user guide, it said psfgen
>>>>>>>>>>>>> will
>>>>>>>>>>>>> patch N-terminal and C-terminal atoms. What does "patch"
>>>>>>>>>>>>> means? Do these
>>>>>>>>>>>>> termini carry charges?
>>>>>>>>>>>>> Thank you.
>>>>>>>>>>>>> Sincerely,
>>>>>>>>>>>>> Margaret S. Cheung,
>>>>>>>>>>>>> Ph. D. Postdoctoral Fellow,
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> ------------------------------------------------------------
>>>>>>>>>>>>> Room 2117 Tel: (301) 405-4892
>>>>>>>>>>>>> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
>>>>>>>>>>>>> University of Maryland http://glue.umd.edu/~mscheung
>>>>>>>>>>>>> College Park, MD 20742-2431 email:
>>>>>>>>>>>>> mscheung_at_ipst.umd.edu
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> ------------------------------------------------------------
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> NIH Resource for Macromolecular Modeling and
>>>>>>>>>>>> Bioinformatics
>>>>>>>>>>>> Beckman Institute for Advanced Science and Technology
>>>>>>>>>>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL
>>>>>>>>>>>> 61801
>>>>>>>>>>>> Email: johns_at_ks.uiuc.edu Phone:
>>>>>>>>>>>> 217-244-3349
>>>>>>>>>>>> WWW: http://www.ks.uiuc.edu/~johns/ Fax:
>>>>>>>>>>>> 217-244-6078
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Margaret S. Cheung,
>>>>>>>>>> Ph. D. Postdoctoral Fellow,
>>>>>>>>>>
>>>>>>>>>> ------------------------------------------------------------
>>>>>>>>>> Room 2117 Tel: (301) 405-4892
>>>>>>>>>> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
>>>>>>>>>> University of Maryland http://glue.umd.edu/~mscheung
>>>>>>>>>> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
>>>>>>>>>> ------------------------------------------------------------
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>> Margaret S. Cheung,
>>>>>>>> Ph. D. Postdoctoral Fellow,
>>>>>>>>
>>>>>>>> ------------------------------------------------------------
>>>>>>>> Room 2117 Tel: (301) 405-4892
>>>>>>>> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
>>>>>>>> University of Maryland http://glue.umd.edu/~mscheung
>>>>>>>> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
>>>>>>>> ------------------------------------------------------------
>>>>>>>>
>>>>>>>
>>>>>>> Margaret S. Cheung,
>>>>>>> Ph. D. Postdoctoral Fellow,
>>>>>>>
>>>>>>> ------------------------------------------------------------
>>>>>>> Room 2117 Tel: (301) 405-4892
>>>>>>> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
>>>>>>> University of Maryland http://glue.umd.edu/~mscheung
>>>>>>> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
>>>>>>> ------------------------------------------------------------
>>>>>>>
>>>>>>
>>>>>> Margaret S. Cheung,
>>>>>> Ph. D. Postdoctoral Fellow,
>>>>>>
>>>>>> ------------------------------------------------------------
>>>>>> Room 2117 Tel: (301) 405-4892
>>>>>> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
>>>>>> University of Maryland http://glue.umd.edu/~mscheung
>>>>>> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
>>>>>> ------------------------------------------------------------
>>>>>
>>>>>
>>>>>
>>>>
>>>> Margaret S. Cheung,
>>>> Ph. D. Postdoctoral Fellow,
>>>>
>>>> ------------------------------------------------------------
>>>> Room 2117 Tel: (301) 405-4892
>>>> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
>>>> University of Maryland http://glue.umd.edu/~mscheung
>>>> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
>>>> ------------------------------------------------------------
>>>
>>>
>>
>> Margaret S. Cheung,
>> Ph. D. Postdoctoral Fellow,
>>
>> ------------------------------------------------------------
>> Room 2117 Tel: (301) 405-4892
>> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
>> University of Maryland http://glue.umd.edu/~mscheung
>> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
>> ------------------------------------------------------------
>
Margaret S. Cheung,
Ph. D. Postdoctoral Fellow,
------------------------------------------------------------
Room 2117 Tel: (301) 405-4892
Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
University of Maryland http://glue.umd.edu/~mscheung
College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
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