From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Nov 19 2021 - 03:32:39 CST
Hi Peter
Bonds between all couple of atoms, even CL-CL
> 5000 !NBOND: bonds
> 1 2 1 4 1 5 1
> 6
> 2 3 7 8 7 10 7
> 11
> 7 12 8 9 13 14 13
> 16
> 13 17 13 18 14 15 19
> 20
> 19 22 19 23 19 24 20
> 21
>
where atom numbering is
> 5000 !NATOM
> 1 AO1 1 CCL3 C CCM 0.179000 12.0110 0
> 2 AO1 1 CCL3 CL1 CLCM -0.087000 35.4500 0
> 3 AO1 1 CCL3 CL2 CLCM -0.087000 35.4500 0
> 4 AO1 1 CCL3 CL3 CLCM -0.087000 35.4500 0
> 5 AO1 1 CCL3 HX HCM 0.082000 1.0080 0
>
> All such bonding is also evident from loading psf/pdb to vmd.
>
> I started from a box prepared with packmol, and I tried also adding TER
> between residues
> HEADER
> TITLE Built with Packmol
> REMARK Packmol generated pdb file
> REMARK Home-Page: https://urldefense.com/v3/__http://m3g.iqm.unicamp.br/packmol__;!!DZ3fjg!q3HBReG05vAH7TecnLBopbfTkKXY0lAdye4dyLyj39gbbf1ugnRqvHu298tdcTTxSQ$
> REMARK
> HETATM 1 CL1 CCL3A 1 30.522 5.429 3.173 1.00 0.00
> CL
> HETATM 2 CL2 CCL3A 1 30.670 3.053 4.852 1.00 0.00
> CL
> HETATM 3 CL3 CCL3A 1 31.018 2.823 1.969 1.00 0.00
> CL
> HETATM 4 C CCL3A 1 31.285 3.845 3.391 1.00 0.00
> C
> HETATM 5 HX CCL3A 1 32.361 3.996 3.509 1.00 0.00
> H
> TER
> HETATM 6 CL1 CCL3A 2 3.817 17.228 1.210 1.00 0.00
> CL
> HETATM 7 CL2 CCL3A 2 1.496 17.919 2.829 1.00 0.00
> CL
> HETATM 8 CL3 CCL3A 2 3.573 16.195 3.922 1.00 0.00
> CL
> HETATM 9 C CCL3A 2 3.231 17.561 2.849 1.00 0.00
> C
> HETATM 10 HX CCL3A 2 3.759 18.439 3.230 1.00 0.00
> H
> TER
>
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No such problems encountered in making a MEOH box, starting from "RESI
MEOH" in CGenFF. Clear, not interacting MEOH molecules where obtained,
with psf indicating only the correct bonds.
With CHARMM36/CGenFF the only source of topology for CHCL3 is
toppar_chloroform_dh.str
I can't understand where I am wrong with CHCL3
Thanks for advice
francesco
On Thu, Nov 18, 2021 at 3:38 PM Peter Freddolino <petefred_at_umich.edu> wrote:
> Have you looked at the bonds in your psf to make sure they are correct?
> This looks like you've hydrogen atoms that have two bonds...
> Best,
> Peter
>
> On Thu, Nov 18, 2021 at 5:42 AM Francesco Pietra <chiendarret_at_gmail.com>
> wrote:
>
>> It seems thatb the str used is inadequate. Alsdo adjusting angles in str,
>> namd assks for dihedrals
>> fp
>>
>> On Thu, Nov 18, 2021 at 9:29 AM Francesco Pietra <chiendarret_at_gmail.com>
>> wrote:
>>
>>> While attempting to minimize a CHCL3 box built from CHARMM36-provided
>>> toppar_chloroform_dh.str, namd crashes
>>>
>>> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS 1 5
>>>> 4)
>>>> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS 1
>>>> 5 4)
>>>>
>>>
>>> Actually, the prm part of the str (which was read by namd) l correctly
>>> furnishes
>>>
>>>> ANGLES
>>>> CLCM CCM CLCM 0.0 111.30
>>>> HCM CCM CLCM 0.0 107.57
>>>>
>>>
>>> Why is namd looking for those wrong angles? The central atom is carbon
>>> not hydrogen.
>>>
>>> Thanks for advice
>>> francesco pietra
>>>
>>
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