Re: vmd-l:namd-l; question about psfgen (param for CT1?)

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Apr 06 2006 - 15:56:07 CDT

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
> ------------------------------------------------------------

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