From: Peter Freddolino (petefred_at_umich.edu)
Date: Fri Nov 19 2021 - 07:56:58 CST
Based on the comments in that topology file (which I had to google -- it
would really help to include such things in the mailing list discussion),
it looks like those CL-CL and other problematic bonds are present only for
SHAKE. That suggests to me that this is supposed to be a rigid chloroform
model, which might not be possible in NAMD. Did you check the original
paper (W. Dietz, K. Heinzinger, Ber. Bunsen-Ges. Phys. Chem 1985, 89, 968)
for how this is supposed to be implemented?
Thanks,
Peter
On Fri, Nov 19, 2021 at 4:33 AM Francesco Pietra <chiendarret_at_gmail.com>
wrote:
> 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!rfO_wUWkY1X5XBCTAEnorNJUdxsw_prm7ebIkV8xhw4w-5fPksl3kY3o2LgqhQQ8PA$
>> 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
>>
> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
> 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
>>>>
>>>
This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:12 CST