CHARMM Parameters File Issues

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sairamadugu
CHARMM Parameters File Issues

Hello All,

I have a protein-ligand system that I downloaded from PDB and generated the PSF, PDB, CRD and ligand RTF and PRM files from Charmm-GUI website. In the QM/MM part where
------------------
# Optimisation
dl-find \
........
.........
atom_types= $types \
atom_charges= $charges \
use_charmm_psf=yes \
charmm_psf_file=step1_pdbreader.psf \
charmm_parameter_file= par_mod_new.inp \
charmm_mass_file= $top ] ] \
active_atoms= {7704 7705 7706 7707 7708 7709 7710 7711 7712 7713 7714 7715 7716 7717 7718 7719 7720 7721 7722 7723 7724 7725 7726 7727 7728 77
29 7730 7731 7732 7733 7734 7735 773} \
list_option=full \
result=opt.c

---------------
I created the file par_mod_new.inp by combining the RTF files from par_all36_cgenff.prm and par_all36m_prot.prm, the ligand .prm and par_all36_prot_heme.prm. I created the RTF files separately for heme and ligand as well since the heme file comes as toppar file, I separated them. However when the above optimization with DL_Find is run, I get the following error:

parameters taken from CHARMM data file: par_mod_new.inp
header: *>>>> CHARMM36 All-Hydrogen Parameter File for Proteins <<<<<<<<<<
header: *>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<<
header: *>>>>>>>>>>>>>>>>>>>>>>>>>> Jan. 2016 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
header: * All comments to the CHARMM web site: www.charmm.org
header: * parameter set discussion forum
header: *
unmatched open quote in list
trap

ChemShell exiting code 1
the following objects are still declared:

*dl-find.coo fragment 3 main CHARMM import
*dl-find.energy matrix 2 main Scratch energies for dl-find interface
*dl-find.gradient matrix 2 main Scratch gradient for dl-find interface
* charmm.c fragment 1 main CHARMM import
hybrid.conn fragment 2 main CHARMM import
*hybrid.fhi.coords fragment 1 main molecule 6
hybrid.fhi.ener matrix 1 main unnamed
hybrid.fhi.grad matrix 1 main unnamed
hybrid.fhi.iscg matrix 1 main unnamed
*hybrid.dl_poly.coords fragment 1 main molecule 7

while executing
"dlf_c "
(procedure "dl-find" line 719)

----

Is there a way to resolve this error that says "unmatched open quote in list. trap"?

Can I give a list of prm files and set it with set para { par_all36m_prot.prm par_all36_cgenff.prm }? When I tried this option, it did not work.

Can we use the new all36 charmm parameters at all or should we use the all22 files to use Charmm for QM/MM calculations?

I can provide more details.

Any suggestions would be greatly helpful.

Best regards,
Sai

kakali
Hi,

Hi,
In Tcl ChemShell, unfortunately you can't give a list of parameter files. It has to be combined as one. I think from what I gather you did so but I am not sure how you combined them. Could you just make sure when combining the parameter files that all the bonds are under bonds, angles under angles and so on and there is only one END at the end of the parameter file.
Also kindly check the followings:
1. You can combine all36 protein parameter with all22 heme parameters but make sure that you have the corresponding topology files
2. Also remember that parameters are read chronologically, so if you have 2 parameters describing a bond, the last one will be used. So when combining make sure that such type of duplicities are taken into account
3. Earlier charm used to have a number index with atom type (under MASS) section in topology file. The recent ones doesn't uses the number index in a direct way and they are all set to -1 (MASS section of topology file, and ATOMS in parameter file). In case you still have issues the this might be worth checking. I don't remember if this -1 in the MASS and ATOM section causes issues with TCL chemshell. If you have already taken into account all the above, might be worth taking a look into this issue.

Hope it helps.
Best,
Kakali

sairamadugu
Hello Kakali,

Hello Kakali,

Thank you for your response. In the end I combined the files using a windows based software, VEGA ZZ (https://www.ddl.unimi.it/cms/index.php?Software_projects:VEGA_ZZ). That worked well but I gave up using Charmm and currently trying to use Amber 20 and Ambertools to get the MD part done and use the topology and restart files to run the QM/MM (QM part is done by FHI-Aims). I will post another message with the errors I am getting.

Best,
Sai

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