From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Thu Apr 16 2020 - 23:15:34 CDT
It’s in the NBFIX lines of the CGenFF parameter file. I once tried looking into the NAMD code to figure out how to avoid this problem, but the logic was a little more complex than I expected and I gave up. You can either include the related file(s), comment the line out, or make a separate file with just the vdW for any NBFIXed atom types.
Best,
JC
> On Apr 15, 2020, at 4:55 PM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
>
> Hi Mariano
>
> Rerun by adding
> toppar_all36_carb_glycolipid.str
> toppar_all36_carb_glycopeptide.str
>
> and, to the ligand vdW in the .str:
>
> OC2D1 0.00 0.000 0.000
>
> it asked for OC2D2
>
> OC2D2 0.00 0.000 0.000
>
> it asked for
> OC2D3
>
> OC2D3 0.00 0.000 0.000
>
> it asked for OC2D4
>
> OC2D4 0.00 0.000 0.000
>
> now minimization went to completion regularly.
>
> However, none of these atom types were accounted for, see the namd log excerpt
>
> PREVIOUS VALUES sigma=3.65268 epsilon=0.078 sigma14=3.38542 epsilon14=0.01
> USING VALUES sigma=3.65268 epsilon=0.078 sigma14=3.65268 epsilon14=0.078
> Info: SKIPPING rtf SECTION IN STREAM FILE
> Info: SKIPPING rtf SECTION IN STREAM FILE
> Info: SUMMARY OF PARAMETERS:
> Info: 968 BONDS
> Info: 2885 ANGLES
> Info: 6702 DIHEDRAL
> Info: 223 IMPROPER
>
> the structure after minimization is OK.
> There is a iodine atom substituent at sp2 carbon in the ligand and I had to manipulate the .str, removing what concerns lone pair and therefore adjusting the charges. perhaps that has confused namd, but it is unclear. Unclear also whether the toppar for glyco are really needed, but I did not check further.
>
> I'll place the ligand with the QM atoms for QMMM, so that I was not much interested in its .str
>
> I have no good mind for making a minimal set
>
> regards
> francesco
>
>
> On Wed, Apr 15, 2020 at 5:54 PM Mariano Spivak <marspivak_at_gmail.com <mailto:marspivak_at_gmail.com>> wrote:
> Hello Francesco,
>
> If you would like to share a minimal set of files to reproduce this error, I can take a look and help you.
>
> Best regards
>
> Mariano Spivak, Ph.D.
> Theoretical and Computational Biophysics Group
>
> Beckman Institute, University of Illinois.
>
> mariano_at_ks.uiuc.edu <mailto:mariano_at_ks.uiuc.edu>
> mspivak_at_illinois.edu <mailto:mspivak_at_illinois.edu>
>
> On Wed, Apr 15, 2020 at 10:34 AM Francesco Pietra <chiendarret_at_gmail.com <mailto:chiendarret_at_gmail.com>> wrote:
> Hello
> As you can see from the log file below, namd 2.13, on minimization, complains about the lack of vdW for atom type OC2D1. Actually such atom type, if it exists at all, is not present in either the .str file for my ligand or the general .psf file for my receptor made of nuclei/prot, on attempt to minimization, generated with CHARMM36 FF jul19, i.e the latest, which includes CGenFF 4.3.
>
> As I plan to carry out QMMM, I added the to the .str vdW the line
> OC2D1 0.00 0.000 0.000
> getting the same request of vdW for atom type OC2D1
>
> Warning: DUPLICATE vdW ENTRY FOR IGR1
> PREVIOUS VALUES sigma=3.99123 epsilon=0.52 sigma14=3.99123 epsilon14=0.52
> USING VALUES sigma=3.52796 epsilon=0.23 sigma14=3.52796 epsilon14=0.23
> Warning: DUPLICATE vdW ENTRY FOR CG3RC1
> PREVIOUS VALUES sigma=3.56359 epsilon=0.032 sigma14=3.38542 epsilon14=0.01
> USING VALUES sigma=3.56359 epsilon=0.032 sigma14=3.56359 epsilon14=0.032
> Warning: DUPLICATE vdW ENTRY FOR NG2S1
> PREVIOUS VALUES sigma=3.29633 epsilon=0.2 sigma14=2.76179 epsilon14=0.2
> USING VALUES sigma=3.29633 epsilon=0.2 sigma14=3.29633 epsilon14=0.2
> Warning: DUPLICATE vdW ENTRY FOR CG3C52
> PREVIOUS VALUES sigma=3.59923 epsilon=0.06 sigma14=3.38542 epsilon14=0.01
> USING VALUES sigma=3.59923 epsilon=0.06 sigma14=3.59923 epsilon14=0.06
> Warning: DUPLICATE vdW ENTRY FOR OG2D1
> PREVIOUS VALUES sigma=3.02906 epsilon=0.12 sigma14=2.49452 epsilon14=0.12
> USING VALUES sigma=3.02906 epsilon=0.12 sigma14=3.02906 epsilon14=0.12
> Warning: DUPLICATE vdW ENTRY FOR CG331
> PREVIOUS VALUES sigma=3.65268 epsilon=0.078 sigma14=3.38542 epsilon14=0.01
> USING VALUES sigma=3.65268 epsilon=0.078 sigma14=3.65268 epsilon14=0.078
> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OC2D1
>
> thanks for advice
> francesco pietra
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