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From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Jan 20 2022 - 08:31:36 CST

Mail sent inadvertently before adding

Thanks for advice
francesco pietra

---------- Forwarded message ---------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Thu, Jan 20, 2022 at 9:26 AM
Subject: Problems with charmm36 modified nucleotides for psfgen and namd
To: NAMD <namd-l_at_ks.uiuc.edu>, VMD Mailing List <vmd-l_at_ks.uiuc.edu>

Hi all
I am encountering problems to run MD on latest namd with charmm36 modified
nucleotides. psf/pdb generated on latest vmd text with psfgen (autopsfgen
does not understand modified nucleotides, as I posted recently)

The problems concerns the structure of the "small molecule" ligand
surrounded bu nucleotides, and in small part by proteins.

The "small molecule" parameterized at the MATCH server, in TIP3 water
performs very well under MD on the basis of solely its MATCH-generated rpm
(plus water/ions prm). When embodied (non bonded) in the nucleotide system,
it undergoes structural distortions, mainly angle/dihedral at sp3 carbons
(methyl groups), but also at CH2 groups, and the benzene ring become s
heavily non planar. The carbon backbone has a correct bonding sequence.

In my understanding, parameters are being mixed. "grep -r atomname" at the
used parameters shows that only params from MATCH are used for non
distorted atoms

>
> francesco_at_vaio:~/tmp$ grep -r O301
> HMT.prm:C331 O301 360.00 1.4150
> HMT.prm:C251 O301 450.00 1.3710
> HMT.prm:C251 C251 O301 130.00 111.70
> HMT.prm:HGA3 C331 O301 45.90 108.89
> HMT.prm:C331 O301 C251 65.00 108.00
> HMT.prm:CC51 C251 O301 75.70 110.10
> HMT.prm:O301 C251 C251 CRC1 8.8900 2 180.00
> HMT.prm:HG51 C251 C251 O301 4.5000 2 180.00
> HMT.prm:C251 C251 O301 C331 0.2700 2 0.00
> HMT.prm:C251 C251 O301 C331 0.0000 3 0.00
> HMT.prm:C251 C251 O301 C331 0.2000 1 0.00
> HMT.prm:HGA3 C331 O301 C251 0.0850 3 0.00
> HMT.prm:C331 O301 C251 CC51 1.6500 2 180.00
> HMT.prm:C331 O301 C251 CC51 0.4500 3 0.00
> HMT.prm:C331 O301 C251 CC51 0.1000 1 180.00
> HMT.prm:O302 CC51 C251 O301 0.2000 3 0.00
> HMT.prm:CRC1 CC51 C251 O301 0.0000 3 0.00
> HMT.prm:HGA1 CC51 C251 O301 0.1950 3 0.00
> HMT.prm:O301 0.0000 -0.1000 1.6500
> HMT.rtf:MASS 142 O301 15.99900 O
> HMT.rtf:ATOM O3 O301 -0.310000
>

while for atoms that become distorted, params from elsewhere are probably
also taken

francesco_at_vaio:~/tmp$ grep -r C331
> HMT.prm:C331 O301 360.00 1.4150
> HMT.prm:C331 HGA3 322.00 1.1110
> HMT.prm:C331 O302 340.00 1.4300
> HMT.prm:C301 C331 222.50 1.5380
> HMT.prm:HGA3 C331 O301 45.90 108.89
> HMT.prm:C331 O301 C251 65.00 108.00
> HMT.prm:HGA3 C331 HGA3 35.50 108.40
> HMT.prm:C2O2 O302 C331 40.00 109.60
> HMT.prm:HGA3 C331 O302 60.00 109.50
> HMT.prm:C331 C301 C321 58.35 113.50
> HMT.prm:C331 C301 C331 58.35 113.50
> HMT.prm:O311 C301 C331 75.70 110.10
> HMT.prm:C301 C331 HGA3 33.43 110.10
> HMT.prm:C251 C251 O301 C331 0.2700 2 0.00
> HMT.prm:C251 C251 O301 C331 0.0000 3 0.00
> HMT.prm:C251 C251 O301 C331 0.2000 1 0.00
>
HMT.prm:HGA3 C331 O301 C251 0.0850 3 0.00
> HMT.prm:C331 O301 C251 CC51 1.6500 2 180.00
> HMT.prm:C331 O301 C251 CC51 0.4500 3 0.00
> HMT.prm:C331 O301 C251 CC51 0.1000 1 180.00
> HMT.prm:C331 O302 C2O2 C321 2.0500 2 180.00
> HMT.prm:C331 O302 C2O2 O2D1 3.8500 2 180.00
> HMT.prm:C331 O302 C2O2 O2D1 0.9650 1 180.00
> HMT.prm:C2O2 O302 C331 HGA3 0.0000 3 0.00
> HMT.prm:C321 C321 C301 C331 0.2000 3 0.00
> HMT.prm:HGA3 C331 C301 C321 0.1600 3 0.00
> HMT.prm:C331 C301 C321 HGA2 0.1950 3 0.00
> HMT.prm:HGA3 C331 C301 C331 0.1600 3 0.00
> HMT.prm:HGP1 O311 C301 C331 0.1400 2 0.00
> HMT.prm:HGP1 O311 C301 C331 0.2400 3 0.00
> HMT.prm:HGP1 O311 C301 C331 1.1300 1 0.00
> HMT.prm:O311 C301 C331 HGA3 0.1400 3 0.00
> HMT.prm:C331 0.0000 -0.0780 2.0500
>
par_all36_carb.prm:MASS -1 CC331 12.01100 ! generic acyclic CH3
> carbon (xyl C6, glcna/galna CT)
> par_all36_carb.prm:CC2O3 CC331 330.00 1.500 ! ketone MP2/6-31g*,
> CSD geometry
> par_all36_carb.prm:CC2O4 CC331 250.00 1.500 ! acetaldehyde, adm
> par_all36_carb.prm:CC301 CC331 222.50 1.538 ! genff CG301 CG331
> par_all36_carb.prm:CC311 CC331 222.50 1.538 ! par22 CT3 CT1
> par_all36_carb.prm:CC331 CC3163 222.50 1.538 ! par22 CT3 CT1 og
> xtal alfuco
> par_all36_carb.prm:CC2O1 CC331 250.00 1.520 ! og ipaa and xtal
> acglua11 agalam10 nacman10
> par_all36_carb.prm:CC321 CC331 222.50 1.528 ! par22 CT3 CT2
> par_all36_carb.prm:CC331 OC311M 428.00 1.420 ! par22 OH1 CT3
> par_all36_carb.prm:CC331 OC301 360.00 1.415 ! par35 CC33A OC30A
> par_all36_carb.prm:NC2D1 CC331 320.00 1.430 ! par22 NH1 CT3
>
etc, long list

Even using the ParamChem-CGenFF server (generating .str to be used with
CGenFF parameters v 4.5, while I used v 4.6 because 4.5 does not exist)
same issue.