Hi Lizelle,
I am not very familiar with the atom recognition in VMD, maybe Dave has more ideas about it.
Kind regards,
Pengfei
> On Jul 11, 2017, at 5:50 AM, Lizelle Lubbe <LBBLIZ002.myuct.ac.za> wrote:
>
> Dear Pengfei and David,
>
> Thanks for the helpful information.
>
>> The PDB standard is to put the element into columns 77-78 of the ATOM or HETATM line. Are you perhaps using an old version of AmberTools?
> I am using AmberTools 15
>
>> I'm somewhat confused here: PDB files don't contain any hybridization information in them. It sounds like you may be describing the hybridization assigned by the visualization program.
> Yes, I was describing the visualization program's assignment, but it probably doesn't matter then since I'm using the mol2 and frcmod from MCPB.py
>
>> Use a text editor to check your pdb file, and see if the element information is in the correct place.
> I've checked the leap input pdb file again and although it all seems to be fine (changed Cl- to CL) it still displays a carbon. After running pdb4amber on it, however, it correctly displays a chlorine ion (output pdb attached).
>
> Using this as input for leap gives pdb output files that correctly display a chloride ion with formal charge of -1. The corresponding prmtop and rst7 visualization in VMD still gave C with no charge. Could you please help me to understand why this is the case? Would the ff14SB forcefield correctly type CL instead of C during the MD?
>
> Kind regards
>
> Lizelle Lubbe
>
> PhD (Medical biochemistry) candidate
> Department of Integrative Biomedical Sciences
> University of Cape Town
> ________________________________________
> From: Pengfei Li <ambermailpengfei.gmail.com <mailto:ambermailpengfei.gmail.com>>
> Sent: 11 July 2017 04:27:58 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] tleap atom type and hybridization
>
> Hi Lizelle,
>
> Based on my understanding, the atom types don’t really play a role in the molecular dynamics simulation in AMBER since all the bond linkage information is specified independently.
>
> For the ion recognition in LEaP, this webpage may be helpful: http://ambermd.org/tutorials/advanced/tutorial20/nonbonded_model.htm <http://ambermd.org/tutorials/advanced/tutorial20/nonbonded_model.htm><http://ambermd.org/tutorials/advanced/tutorial20/nonbonded_model.htm <http://ambermd.org/tutorials/advanced/tutorial20/nonbonded_model.htm>>.
>
> Kind regards,
> Pengfei
>
>> On Jul 10, 2017, at 7:13 AM, Lizelle Lubbe <LBBLIZ002.myuct.ac.za> wrote:
>>
>>
>> Dear Amber users,
>>
>> I want to perform MD simulations on a glycoprotein with an active site zinc (+2), water and chloride ion (-1).
>>
>> The metal site (ZN, water, HD1, HD2, OE1) forcefield parameters were determined using MCPB.py. The hybridization is correctly specified in the frcmod file (HD1, HD2, OE1 sp2) but when visualizing the pdb (saved from the prmtop and rst7 of tleap) it doesn't correspond (HD1 sp3, HD2 sp2, OE1 sp3, ZN sp2, Water sp3). Can I assume that it is in fact correctly given as the aforementioned and that the conversion to pdb just doesn't capture this correctly? Or should it be set in the tleap.in file at AddAtomTypes by changing sp3?
>>
>> addAtomTypes {
>> { "X1" "N" "sp3" }
>> { "X2" "N" "sp3" }
>> { "X3" "O" "sp3" }
>> { "Z1" "Zn" "sp3" }
>> { "X4" "O" "sp3" }
>> }
>>
>> Is there any way to inspect the atom hybridization in AMBER?
>>
>> Since glycan addition removed the chloride ion, I copied its coordinates from the deposited pdb into the Amber-format glycoprotein pdb. The chloride atom type was set to Cl- as shown below
>>
>> HETATM12492 H2O 0fA 720 -35.331 -14.332 -7.397 1.00 0.00 H
>> TER
>> HETATM12493 ZN ZN1 721 -27.766 -21.998 -36.628 1.00 0.00 Zn
>> TER
>> HETATM12494 Cl- Cl- 722 -18.015 -27.711 -36.880 1.00 0.00 Cl-
>> TER
>> ATOM 12495 O WT1 723 -27.107 -20.515 -34.545 1.00 0.00 O
>> ATOM 12496 H1 WT1 723 -26.150 -20.515 -34.545 1.00 0.00 H
>> ATOM 12497 H2 WT1 723 -27.347 -19.588 -34.545 1.00 0.00 H
>> TER
>> END
>>
>> The atomic_ions.lib file lists Cl- so I assumed this was correct but when visualizing the tleap output as pdb (generated from prmtop and rst7) in UCSF Chimera and Discovery Studio, the atomtype is given as a carbon (sp3) with no formal charge. Is there a way to inspect the Cl- atom in tleap? (I've tried desc from the manual but new to AMBER and not sure how to use it)
>>
>> What is the correct way to insert a chloride ion in AMBER format?
>>
>> Kind regards
>>
>> Lizelle Lubbe
>>
>> PhD (Medical biochemistry) candidate
>> Department of Integrative Biomedical Sciences
>> University of Cape Town
>> Disclaimer - University of Cape Town This e-mail is subject to UCT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. If this e-mail is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via csirt.uct.ac.za
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> <11072017_NDOM_cat_noLINK_CLedit_RENUM.pdb>
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Received on Thu Jul 13 2017 - 12:30:04 PDT
