From: Pratik Narain Srivastava (pratik.narain_at_gmail.com)
Date: Wed Apr 15 2020 - 10:48:04 CDT
I can't pinpoint whether it's a problem or not but the charmm36 force
fields require you to add all the strs to psfgen and prms to the namd
configuration file. For example, your concerned atom type is present in the
glycopeptide and glycolipid str files in the charmm36 ff. What i do is add
all the str files when generating PSF and all the corresponding prms as
well as the waters str in the config file.
Regards
On Wed, Apr 15, 2020, 9:01 PM Francesco Pietra <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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