VMD-L Mailing List

From: Amy Rice (arice3_at_hawk.iit.edu)
Date: Tue Sep 22 2015 - 11:26:48 CDT

Thank you for the help! I have gone back and included the protein and CGen
files when creating the initial parameter file as suggested, and that made
things much easier. This time, I was able to complete the charge
optimization without encountering the error I had before. I did have a
question about this step though. It appears from the top_all36_prot.rtf
that the backbone charges (and even some of the side chains, such as CB and
CG in the residues with longer side chains) are all standardized. I
excluded all the aliphatic hydrogens from the optimization, as explained in
the screencast tutorials. I decided also to exclude the backbone atoms and
use the partial charges as given in the arginine residue. Would you
recommend excluding more of the atoms (CB and CG, maybe CD), or including
everything in the charge optimization?

On Thu, Sep 17, 2015 at 4:21 PM, Mayne, Christopher G <cmayne2_at_illinois.edu>
wrote:

> Amy,
>
> I'm not quite sure what's going on here. It seems like it's looking for
> an atom type that is a concatenation of several atoms, and I'm not sure why
> it would do that since you're PSF seems OK. I can come back to this
> problem, but I see a couple of other issues here.
>
> Based on the contents of your initial PAR file I can tell that you didn't
> include the par_all36_prot.prm file as an "associated parameter file".
> Many of the parameters that you have in your PAR file are defined by the
> standard CHARMM force field for proteins. Including this file when
> generating the initial parameter file will significantly reduce the number
> of missing parameters that you will have to work on.
>
> You should check out the CGenFF topology file, specifically how residue
> GUA changes to MGUA. Comparing these two entries will be helpful in
> assessing the changes associated with methylating the nitrogens of
> guanidinium, e.g., how the partial atomic charges change, and it will give
> you proper LJ parameters for the terminal methyl. Many of the missing
> parameters should be defined, albeit in CGenFF terms (i.e., using CGenFF
> atom types rather than CHARMM protein atom types). It may be a little
> tedious, but you should be able to translate these.
>
> Anything that remains missing won't required parameterizing the full
> molecule that you've constructed. At worst you can truncate the system
> to an N-methyl and N-propyl guanidinium.
>
>
> Regards,
> Christopher Mayne
>
>
>
>
> On Sep 17, 2015, at 2:39 PM, Amy Rice wrote:
>
> Hi all,
> I am attempting to parameterize a modified arginine residue following the
> ffTK screencasts, using VMD 1.9.2. I've been able to complete the first 4
> steps without issue, but I'm running into some errors during the charge
> optimization, in both downhill mode and simulated annealing. The error
> message reads:
> "can't read "ljPars(HA2 HA2 HA2 H)": no such element in array"
>
> I noticed a similar problem was discussed previously (
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22158.html
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_Research_vmd_mailing-5Flist_vmd-2Dl_22158.html&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=KWvVUHl42S-_kpj6OunU5-512j104OJKVMt2MxKKoE8&m=Kwb2Jbxuzl6mrlGjt2VMpN6KFhUmTiXF98tNadaBt6I&s=rzmQTVqd5MIv2Uvb5uXTXzAXLtFdd2Ar41qkzKLTsnM&e=>),
> however as far as I can tell the atom types HA2 and H exist in both the psf
> and parm files. I have LJ parameters in my .par file for both of these atom
> types, so I'm not sure why I'm receiving an error. I've attached my
> preliminary psf, pdb, and par for reference. Note that I am also loading
> the charmm 36 protein prm as an input paramter file.
>
> Thank you for the help,
> - Amy
>
> --
> Amy Rice
> Ph.D. Student
> Physics Department
> Illinois Institute of Technology
> <m_arginine_files.zip>
>
>
> 

-- 
Amy Rice
Ph.D. Student
Physics Department
Illinois Institute of Technology