Dear Kellon,
As it came out, my mistake is rather simple:
I only loaded part of force field through loadoff, not whole modified
forcefield.
source leaprc.protein.ff19SB
*loadoff $AMBERSOURCE/dat/leap/lib/mod_amino19.lib*
prot = loadpdb ./1pl6_prep.pdb
check prot
<parameter errors>
Once I used:
*source leaprc.protein.ff19SB_modAA*
and modified pdb file accordingly to your suggestions, I was able to generate topology and input coordinates.
Thank you very much!
Rafal
On 15.05.2021 23:23, Kellon Belfon wrote:
> 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
>>>>>
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Received on Sat May 15 2021 - 15:30:02 PDT
