From: Margaret Shun Cheung (mscheung_at_ipst.umd.edu)
Date: Thu Apr 06 2006 - 16:08:25 CDT
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
------------------------------------------------------------
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