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

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Apr 06 2006 - 16:25:30 CDT

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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:43:29 CST