Hi,

I need to generate the psf and crd files for a ligand molecule (which I only have its data in pdb format). Since we think that that academic charmm does not have the capability to generate parameters for arbitrary drug-like molecules of our ligand sort, I need somehow to get the psf and crd files and so can move on to the next step.

I appreciate if you let me know of any solution.

Below please find the data (in pdb format) for my ligand.

ATOM 1 N AZP 1 -24.463 -37.540 5.040 1.00 0.00 A
ATOM 2 CAI AZP 1 -25.349 -36.905 5.824 1.00 0.00 A
ATOM 3 OAH AZP 1 -24.798 -36.098 6.903 1.00 0.00 A
ATOM 4 CAG AZP 1 -25.834 -35.506 7.695 1.00 0.00 A
ATOM 5 CAE AZP 1 -26.575 -34.360 7.018 1.00 0.00 A
ATOM 6 CAD AZP 1 -26.069 -33.058 7.092 1.00 0.00 A
ATOM 7 CAC AZP 1 -26.782 -32.005 6.492 1.00 0.00 A
ATOM 8 CAB AZP 1 -27.999 -32.258 5.839 1.00 0.00 A
ATOM 9 CAA AZP 1 -28.505 -33.570 5.765 1.00 0.00 A
ATOM 10 CAF AZP 1 -27.787 -34.628 6.339 1.00 0.00 A
ATOM 11 OAL AZP 1 -26.572 -36.947 5.612 1.00 0.00 A
ATOM 12 CA AZP 1 -24.796 -38.339 3.845 1.00 0.00 A
ATOM 13 CB AZP 1 -24.359 -37.516 2.644 1.00 0.00 A
ATOM 14 CG AZP 1 -24.313 -38.288 1.338 1.00 0.00 A
ATOM 15 CD1 AZP 1 -25.696 -38.134 0.694 1.00 0.00 A
ATOM 16 CD2 AZP 1 -23.262 -37.638 0.420 1.00 0.00 A
ATOM 17 C AZP 1 -24.082 -39.645 4.008 1.00 0.00 A
ATOM 18 O AZP 1 -22.857 -39.753 4.176 1.00 0.00 A
ATOM 19 NAS AZP 1 -24.797 -40.729 4.062 1.00 0.00 A
ATOM 20 CAT AZP 1 -24.122 -42.011 4.245 1.00 0.00 A
ATOM 21 CAV AZP 1 -25.151 -43.125 4.083 1.00 0.00 A
ATOM 22 CAW AZP 1 -26.009 -43.280 5.326 1.00 0.00 A
ATOM 23 CBF AZP 1 -25.445 -43.281 6.603 1.00 0.00 A
ATOM 24 CBG AZP 1 -26.288 -43.503 7.714 1.00 0.00 A
ATOM 25 CBH AZP 1 -27.663 -43.746 7.541 1.00 0.00 A
ATOM 26 CBI AZP 1 -28.210 -43.809 6.284 1.00 0.00 A
ATOM 27 CBJ AZP 1 -27.390 -43.585 5.174 1.00 0.00 A
ATOM 28 CAU AZP 1 -23.048 -42.180 3.189 1.00 0.00 A
ATOM 29 OAY AZP 1 -23.253 -41.797 2.062 1.00 0.00 A
ATOM 30 NAX AZP 1 -21.881 -42.752 3.473 1.00 0.00 A
ATOM 31 NAZ AZP 1 -20.915 -43.024 2.400 1.00 0.00 A
ATOM 32 CBA AZP 1 -19.721 -42.199 2.224 1.00 0.00 A
ATOM 33 CBB AZP 1 -20.156 -40.916 1.556 1.00 0.00 A
ATOM 34 CBC AZP 1 -18.937 -40.097 1.270 1.00 0.00 A
ATOM 35 NBE AZP 1 -18.820 -39.414 0.130 1.00 0.00 A
ATOM 36 OBD AZP 1 -18.056 -40.142 2.118 1.00 0.00 A
ATOM 37 CBK AZP 1 -21.032 -44.155 1.692 1.00 0.00 A
ATOM 38 OBL AZP 1 -20.420 -44.290 0.613 1.00 0.00 A
ATOM 39 CBM AZP 1 -22.067 -45.185 2.152 1.00 0.00 A
ATOM 40 CBO AZP 1 -22.821 -45.685 0.913 1.00 0.00 A
ATOM 41 OBN AZP 1 -23.490 -44.509 0.459 1.00 0.00 A
ATOM 42 CBP AZP 1 -23.922 -46.676 1.292 1.00 0.00 A
ATOM 43 OBQ AZP 1 -23.850 -47.899 1.176 1.00 0.00 A
ATOM 44 OBR AZP 1 -25.136 -46.126 1.824 1.00 0.00 A
ATOM 45 CBS AZP 1 -25.997 -47.149 2.361 1.00 0.00 A
ATOM 46 CBT AZP 1 -26.857 -46.319 3.305 1.00 0.00 A
TER 47 AZP 1
END



Thanks!
Sarvin Moghaddam, Ph.D.
CARB Research Associate
Center for Advanced Research in Biotechnology
University of Maryland Biotechnology Institute

Your post was added some time ago, but perhaps this reply will be of use to either you or others anyway. This is a common problem. One benefit of a graphical/visual interface such as Discovery Studio, Insight II, or Quanta is that the user can sketch a molecule (for example a non-standard residue) set bond orders and then add atom types and charges from the selected force field. In addition, Discovery Studio (v 2.5.5)now has significantly extended abilities to automatically generate force field parameters when that is necessary if that option is selected in the preferences menu.

After a force field has been applied to a molecule the crd and psf can be exported. Our legacy products Insight II and Quanta have similar ability. DS 2.5.5 also has the ability to save the rtf and prm information as a custom template which can be automatically applied the next time a residue with that name is encountered.

If you need more information please contact support@accelrys.com

Regards,
Ken

On the other hand, the academic force fields have evolved considerably since the post, esp. the newer CGenFF (see Parameter forum) which was implemented to meet this type of need within academic CHARMM.

I have some doubt that automatic parameters from DS 2.5.5 are appropriate for use with the biopolymer force fields in CHARMM; one should be careful about playing mix and match with parameter sets with different origins and development philosophy.

Rick,
I have 450 drugs in mol2 and pdb format that I want to import into charmm to do coordinate analysis with. Namely, I want to coor orient them and then take the highest |Y| coordinate as the second elliptical diameter (waist size) of the drugs. I wrote a charmm stream file to do this as a loop using incremental filenaming, if I can get the molecules read in. SwissParm allows me convert mol2 to psf and cor one-at-a-time, and Vincent Zoete has offered to write a script to convert them in a batch. My question is: without rtf files (mass definitions), what good will Vincent's psf and cor files do me? Can charmm do coordinate manipulations without reading residue and topology files?

I certainly suspect CHARMM may have a problem with reading a PSF without the appropriate RTF/PARAM file pairs. For that problem and that many molecules, I'd probably consider learning Python, which already has libraries for "PDB objects" (and maybe mol2 as well). I think the CACTVS suite may be another possibility.

Rick, Thanks for the quick reply. I haven't yet tried Python or CACTVS suite. Nor have I been able to find CgenFF. However, I did use SwissParam.com to convert one mol2 file. It's pretty cool: the server quickly returns good looking rtf, param, psf, and pdb (and itp, whatever that is) files which I had no trouble reading in charmm. Now, if they will just set things up to do it for a batch of mol2 files, my needs will be met. I can't vouch for the quality of the parameters - no basis yet.

There are pointers to the CGenFF force field and tutorial in the Parameters forum. There is also a discussion there about the SwissParam server, and appropriate caveats about the parameters.

IHMO, SwissParam may be adequate for an initial screening, while I'd suggest the CGenFF route for more detailed simulations.

Thanks. I found the introduction to CGenFF here:
http://www.charmm.org/ubbthreads-7-5-5/u...=true#Post23479