Hi
Thank you for your answers.
I try to use the prep and frcmod get it from data base ( added in this email), for the group heme (UNIT HEM)
I arrive at the end of the construction of the .top and .crd with the new parameters but I couldn't save it
due to appear that error :
Checking parameters for unit '3hs5_B'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 47
Unit is OK.
> saveamberparm 3hs5_B 3hs5_B.top 3hs5_B.rst
Checking Unit.
Building topology.
Building atom parameters.
For atom: .R<HEM 556>.A<NA 2> Could not find vdW (or other) parameters for type: NP
For atom: .R<HEM 556>.A<NB 23> Could not find vdW (or other) parameters for type: NO
For atom: .R<HEM 556>.A<NC 39> Could not find vdW (or other) parameters for type: NP
For atom: .R<HEM 556>.A<ND 55> Could not find vdW (or other) parameters for type: NO
Parameter file was not saved.
- I don't understand why these vdw are missing. When in the prep file, of the data base, indicates that the NA correspond to a NP ..etc
NA NP S 19 16 14 2.0800 98.0000 90.0000
....
NB NO E 40 38 37 1.3800 124.0000 0.0000
.....
- Also in frcmod appears the corresponding parameters. How can I know which parameters are missing?
Thank you for your help in advanced
Anna
________________________________________
De: Scott Brozell <sbrozell.rci.rutgers.edu>
Enviat el: dijous, 28 d'abril de 2016 19:35
Per a: AMBER Mailing List
Tema: Re: [AMBER] tleap - protein + ligand + heme group
Hi,
On Thu, Apr 28, 2016 at 03:52:13PM +0000, Anna Cebrian Prats wrote:
> I am already working with a protein that have a ligand and a heme cofactor.
> I prepared separate either the ligand and the heme group , in order to obtain the prep and parm files.
> The Heme group I only have the mol2 file and the frcmod. ( I added in this email the corresponding files).
>
> Then, I try to generate the .top and .crd files with tleap, like this:
> > source leaprc.ff14SB
> > source leaprc.gaff
> > loadamberparams FE+3.frcmod
> > loadamberprep FE+3.mol2
> > loadamberparams acd.frcmod
> > loadamberprep acd.in
> > 3hs5 = loadpdb new.pdb ( the pdb of the protein that I check it with pdb4amber)
>
> - The pdb has to contain all (protein structure + ligand + heme group), hasn't it?
> and I obtained this problems:
>
> 1) Unknown residue: HEM number: 552 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
>
> 2) Creating new UNIT for residue: HEM sequence: 553
> One sided connection. Residue: missing connect0 atom.
>
> 3) Created a new atom named: FE within residue: .R<HEM 553>
...
> total atoms in file: 4493
> Leap added 4450 missing atoms according to residue templates:
> 45 Heavy
> 4405 H / lone pairs
> The file contained 43 atoms not in residue templates
>
> One sided connection. Residue: missing connect0 atom.
>
> Why appears all this problems if I enter the prep and parm files?? I know that .mol2 file is not correct , but if i change it to .prep or .in, the Fe atom disappears.
>
> How can I read the mol2 information of Heme group and used to determine structure in the pdb?
You did not show the first clue that something is amiss:
> loadamberprep FE+3.mol2
Loading Prep file: ./FE+3.mol2
Unexpected EOF: discarding residue (73 76 1 0 0)
Checking the tutorials, reading the manual, or searching the list (deeply)
would have lead to using loadMol2 instead of loadamberprep:
HEM = loadMol2 FE+3.mol2
scott
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Received on Fri Apr 29 2016 - 08:30:03 PDT
