Re: Can't find C-PDB bond parameters

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Feb 15 2010 - 12:06:41 CST

You misunderstood. There is an error in the topology file. There is not supposed to be a C - CPB bond to begin with.

On Feb 15, 2010, at 11:44 AM, Francesco Pietra wrote:

> Thanks. Downloaded toppar from
> http://mackerell.umaryland.edu/CHARMM_ff_params.html. Still, I was
> unable to find parameters for the C-CPB bond. In which par file are
> they located? Such params must be somewhere, if not else because of
> "Case Study: Myoglobin Anton Arkhipov, Rosemary Braun and Ying Yin
> February 21, 2008" on the web.
> thanks
> francesco
>
> On Mon, Feb 15, 2010 at 3:15 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
>> Googling "heme cpb bond parameter missing" led me to this: http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=8414&site_id=1#import
>>
>> I'll need to fix the heme topology in the files bundled with VMD. However, this does raise an important point: one should not totally rely on the files distributed in VMD as they are not meant to have complete coverage of the forcefield. It's always best to get the full set of topology and parameters from MacKerell's website.
>>
>>
>> -----Original Message-----
>> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Francesco Pietra
>> Sent: Monday, February 15, 2010 3:46 AM
>> To: vmd; NAMD
>> Subject: namd-l: Can't find C-PDB bond parameters
>>
>> Please disregard my previous thread of similar name. Just to restart
>> from a clean basis.
>>
>> I prepared with VMD 1.8.7 psf and pdb files for a system containing
>> heme (thus, top_all27_prot_lipid_na.inp and
>> par_all27_prot_lipid_na.inp). Solvated and neutralized.
>>
>> NAMD2.7b2 complains that parameters for C - CPB bond are lacking.
>>
>> I checked the structure of my molecule, heme is OK.
>>
>> I checked the top file: bond C - CPB present.
>>
>> I also checked the par file: no C - CPB, as namd complainsed, while
>> parameters for bonds C-CT3, C-CT2, C-CT1, C-CP1, C-C, C-N, C-NC2,
>> C-NH1, C-O are present)
>>
>> As far as I understand, parameters for C-CPB bond (CAB-C3B in atom
>> names, for the bond between a vinyl group and a pyrrole ring) are
>> really lacking.
>>
>> Much indebted for suggestions how to remedy.
>>
>> francesco pietra
>>
>>
>>

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