Hi Rafal,
My attachment did not go through to the listserv because of the size so I
am attaching a link to the folder and the forwarded email from this morning
below.
https://drive.google.com/drive/folders/1Xk3NSztUa9sRsVu1SNW0mGUwTcUA1Ysy?usp=sharing
---------- Forwarded message ---------
From: Kellon Belfon <kellonbelfon.gmail.com>
Date: Sat, May 15, 2021 at 11:40 AM
Subject: Re: [AMBER] Selenomethionine force field parameters
To: AMBER Mailing List <amber.ambermd.org>
Hi Rafal,
I tried on my end with this leap.in script (also tried with ff14SB and
ff14SB_modAA)
source leaprc.protein.ff19SB
source leaprc.protein.ff19SB_modAA
prot = loadpdb ./1pl6_prep.pdb
check prot
saveamberparm prot 1pl6_prep.parm7 1pl6_prep.rst7
Then converted all SE in MSE,AMSE, and BMSE units to SED and removed the
NAD,HOH and ligand (for testing), and run the PDB 1pl6.pdb through
pdb4amber to get the pdb file name 1pl6_prep.pdb
I was able to get the topology file and rst7 file generated. This is with
AmberTools21.
If you do not mind sharing, can you tell me how different your protocol is
from this or share the pdb file you load into leap along with your leap
commands? It would help me reproduce the error on my end.
Thank you!
On Sat, May 15, 2021 at 10:46 AM Kellon Belfon <kellonbelfon.gmail.com>
wrote:
> Hi Rafal,
>
> Can you share with me your leap.in script and which version of ambertools
> you are using?
>
>
>
>
> On Sat, May 15, 2021, 2:59 AM Rafał Madaj <rmadaj.cbmm.lodz.pl> wrote:
>
>> Hi Kellon,
>>
>> I applied changes to pdb files. As long as there are no 'unknown' heavy
>> atoms, there are still some parameters missing:
>>
>> > prot = loadpdb 1pl6_A.pdb
>> Loading PDB file: ./1pl6_A.pdb
>> total atoms in file: 2677
>> Leap added 2735 missing atoms according to residue templates:
>> 2735 H / lone pairs
>> > check prot
>> Checking 'prot'....
>>
>> Warning: The unperturbed charge of the unit (3.066712) is not integral.
>>
>> Warning: The unperturbed charge of the unit (3.066712) is not zero.
>>
>> Warning: Close contact of 1.185506 angstroms between .R<MSE 38>.A<HE3
>> 15> and .R<MSE 38>.A<HA 4>
>>
>> Warning: Close contact of 1.344255 angstroms between .R<SER 158>.A<HB3
>> 7> and .R<THR 302>.A<HG1 12>
>>
>> Warning: Close contact of 0.981188 angstroms between .R<THR 322>.A<HG1
>> 12> and .R<LEU 343>.A<H 2>
>> Checking parameters for unit 'prot'.
>> Checking for bond parameters.
>>
>> Error: Could not find bond parameter for: SE - CT
>>
>> Error: Could not find bond parameter for: SC - H1
>>
>> Error: Could not find bond parameter for: SC - H1
>>
>> Error: Could not find bond parameter for: SC - SE
>>
>> Error: Could not find bond parameter for: 2C - SC
>>
>> Error: Could not find bond parameter for: SE - CT
>>
>> Error: Could not find bond parameter for: SC - H1
>>
>> --- MSE FRAGMENT ---
>>
>> HETATM 278 N MSE A 38 85.991 40.099 50.845 1.00
>> 14.20 N
>> HETATM 279 CA MSE A 38 86.115 39.447 49.549 1.00
>> 14.33 C
>> HETATM 280 C MSE A 38 84.860 38.699 49.126 1.00
>> 15.21 C
>> HETATM 281 O MSE A 38 84.174 38.094 49.952 1.00
>> 14.97 O
>> HETATM 282 CB MSE A 38 87.338 38.533 49.555 1.00
>> 15.33 C
>> HETATM 283 CG MSE A 38 88.609 39.294 49.919 1.00
>> 18.70 C
>> HETATM 284 SED MSE A 38 89.048 40.703 48.611 1.00
>> 21.68 SED
>> HETATM 285 CE MSE A 38 87.500 41.833 48.688 1.00
>> 26.20 C
>>
>> How to deal with that?
>>
>> Best,
>>
>> Rafal
>>
>>
>> On 14.05.2021 02:14, Kellon Belfon wrote:
>> > Hi Rafal,
>> >
>> > I am happy that you are trying out the MSE parameters. I made the
>> decision
>> > to use SED for the atom name of the Selenium based on the position of
>> the
>> > atom. The problem you are having is an atom name issue. Can you change
>> SE
>> > to SED in your pdb file and let me know if that works?
>> >
>> > HETATM 350 SE MSE A 43 51.772 29.090 23.392 1.00 21.41
>> > A SE
>> >
>> > to
>> > HETATM 350 SED MSE A 43 51.772 29.090 23.392 1.00 21.41
>> > A SED
>> >
>> > Best,
>> >
>> > Kellon
>> >
>> > On Thu, May 13, 2021 at 1:51 PM Rafał Madaj <rmadaj.cbmm.lodz.pl>
>> wrote:
>> >
>> >> Dear all,
>> >>
>> >> I am trying to create topology for the protein abundant in
>> >> selenomethionine (MSE). Despite loading additional force field
>> >> parameters (apart from ff19SB and GAFF) - mod_amino19.lib - creating
>> >> topology using tleap returns an error:
>> >>
>> >> > prot = loadpdb rec.pdb
>> >> Loading PDB file: ./rec.pdb
>> >> Created a new atom named: SE within residue: .R<MSE 43>
>> >> Added missing heavy atom: .R<MSE 43>.A<SED 11>
>> >> Created a new atom named: SE within residue: .R<MSE 66>
>> >> Added missing heavy atom: .R<MSE 66>.A<SED 11>
>> >> Created a new atom named: SE within residue: .R<MSE 79>
>> >> Added missing heavy atom: .R<MSE 79>.A<SED 11>
>> >> Created a new atom named: SE within residue: .R<MSE 80>
>> >> Added missing heavy atom: .R<MSE 80>.A<SED 11>
>> >> Created a new atom named: SE within residue: .R<MSE 164>
>> >> Added missing heavy atom: .R<MSE 164>.A<SED 11>
>> >> Created a new atom named: SE within residue: .R<MSE 184>
>> >> Added missing heavy atom: .R<MSE 184>.A<SED 11>
>> >> Created a new atom named: SE within residue: .R<MSE 210>
>> >> Added missing heavy atom: .R<MSE 210>.A<SED 11>
>> >> Created a new atom named: SE within residue: .R<MSE 263>
>> >> Added missing heavy atom: .R<MSE 263>.A<SED 11>
>> >> Created a new atom named: SE within residue: .R<MSE 272>
>> >> Added missing heavy atom: .R<MSE 272>.A<SED 11>
>> >> Added missing heavy atom: .R<CLYS 287>.A<OXT 23>
>> >> total atoms in file: 2269
>> >> Leap added 2239 missing atoms according to residue templates:
>> >> 10 Heavy
>> >> 2229 H / lone pairs
>> >> The file contained 9 atoms not in residue templates
>> >>
>> >> Typical fragment of pdb file containing this residue:
>> >>
>> >> ATOM 337 C ASP A 42 56.212 30.757 19.570 1.00 26.81
>> >> A C
>> >> ATOM 338 O ASP A 42 57.289 30.153 19.632 1.00 26.38
>> >> A O
>> >> ATOM 339 CB ASP A 42 57.337 32.954 19.317 1.00 32.60
>> >> A C
>> >> ATOM 340 CG ASP A 42 57.467 33.033 20.824 1.00 35.76
>> >> A C
>> >> ATOM 341 OD1 ASP A 42 56.474 33.397 21.492 1.00 36.69
>> >> A O
>> >> ATOM 342 OD2 ASP A 42 58.565 32.729 21.341 1.00 39.27
>> >> A O1-
>> >> HETATM 343 N MSE A 43 55.091 30.273 20.097 1.00 22.74
>> >> A N
>> >> HETATM 344 CA MSE A 43 55.098 28.977 20.766 1.00 21.05
>> >> A C
>> >> HETATM 345 C MSE A 43 55.320 27.849 19.773 1.00 18.33
>> >> A C
>> >> HETATM 346 O MSE A 43 54.976 27.967 18.595 1.00 17.94
>> >> A O
>> >> HETATM 347 CB MSE A 43 53.770 28.706 21.472 1.00 22.04
>> >> A C
>> >> HETATM 348 CG MSE A 43 53.342 29.737 22.484 1.00 22.27
>> >> A C
>> >> HETATM 349 CE MSE A 43 52.449 29.121 25.207 1.00 24.40
>> >> A C
>> >> HETATM 350 SE MSE A 43 51.772 29.090 23.392 1.00 21.41
>> >> A SE
>> >> ATOM 351 N THR A 44 55.891 26.753 20.260 1.00 16.37
>> >> A N
>> >> ATOM 352 CA THR A 44 56.108 25.572 19.436 1.00 14.24
>> >> A C
>> >> ATOM 353 C THR A 44 54.771 24.837 19.468 1.00 14.92
>> >> A C
>> >> ATOM 354 O THR A 44 53.898 25.173 20.269 1.00 15.67
>> >> A O
>> >> ATOM 355 CB THR A 44 57.182 24.657 20.039 1.00 13.80
>> >> A C
>> >> ATOM 356 CG2 THR A 44 58.541 25.369 20.072 1.00 11.54
>> >> A C
>> >> ATOM 357 OG1 THR A 44 56.795 24.292 21.370 1.00 11.42
>> >> A O
>> >>
>> >> Do you have any suggestions how to overcome this problem?
>> >>
>> >> Best regards,
>> >>
>> >> Rafal
>> >>
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
--
Kellon A. A. Belfon, Graduate Student
Carlos Simmerling Laboratory
The Laufer Center for Physical and Quantitative Biology
The Department of Chemistry, Stony Brook University
Stony Brook, New York 11794
Phone: (347) 546-4237 <(347)+546+4237> Email: kellon.belfon.stonybrook.
<kellon.belfon.stonybrook.edu>edu
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Received on Sat May 15 2021 - 14:30:02 PDT
