I am not sure what the error means. The coordinate file, PDB in your case, shouldn't have anything but the atom names, residue name, XYZ coordinates.
Delete connectivities at the end.
Could you share, perhaps off the list, the pdb file you have edited along with frcmod and the prepi file?
Best Regards
Elvis Martis
________________________________
From: Sadaf Rani <sadafrani6.gmail.com>
Sent: 27 June 2019 03:00
To: AMBER Mailing List
Subject: Re: [AMBER] open valance problem
Martis
thank you very much for helping me to go through x leap
After editing I saved NADP.frcmod NADP.prepi NADP.pdb
but it gives warning 'dont forget to remove improper dihedrals'
what to do for this?
and will I load this pdb and frcmod file in generating .inprcd and prmtop
files for complex in tleap?
thank you
Sadaf
On Wed, Jun 26, 2019 at 5:53 AM Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> Hello
> Since you did not source the gaff force field, leap threw out those errors.
> Please use the following commands, (I am assuming you are using
> AmbertTools 17 or later)
> xleap
> source leaprc.protein.ff14SB (for protein)
> source leaprc.water.tip3p (for Tip3p waters and counterions)
> sourcc leaprc.gaff
> loadamberparams NADP.frcmod (check if the file name is correct and placed
> in the working directory)
> loadamberprep NADP.prepi
> list (this will show all residue names)
> edit XXX (enter the residue name, here enter the name for NADP)
>
>
> Best Regards
>
> Elvis Martis
>
>
>
> ________________________________
> From: Sadaf Rani <sadafrani6.gmail.com>
> Sent: 25 June 2019 21:59
> To: AMBER Mailing List
> Subject: Re: [AMBER] open valance problem
>
> Dear Martis
> I loaded frcmod & prepi files by using following commands:
>
> mods loadAmberParams NADP.frcmod
> mods2 loadAmberParams NADP.prepi
>
> it shows error as mentioed in screenshot.
>
> Kindly suggest me the right way
>
> thank you
>
> Sadaf
>
> On Tue, Jun 25, 2019 at 6:11 AM Elvis Martis <elvis.martis.bcp.edu.in>
> wrote:
>
> > Hello,
> > you really don't need to obtain the mol2 file this way.
> > I would suggest loading the frcmod and prepi files that you obtained from
> > the Manchester database in xleap.
> > Then see the residue name and atom names for NADP in the database and
> > according modify them in your PDB file (coordinates as complexed with the
> > protein). Once all atoms names and residue names are as per the prepi
> > file, leap should not throw any errors.
> >
> > Hope this helps
> >
> >
> > Best Regards
> >
> > Elvis Martis
> >
> >
> >
> > ________________________________
> > From: Sadaf Rani <sadafrani6.gmail.com>
> > Sent: 25 June 2019 01:55
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] open valance problem
> >
> > Dear Elvis
> >
> > I looked for the NADP parameters as you suggested but I want to get the
> > mol2 file from the same process to loads in to t leap for parameter
> > generation
> > as commands below:-
> >
> > source leaprc.protein.ff14SB
> > source leaprc.gaff2
> > source leaprc.water.tip3p
> >
> > ligA = loadmol2 NAP_amber.mol2
> > ligB = loadmol2 BG6_amber.mol2
> >
> > loadamberparams NAP_amber.frcmod
> > loadamberparams BG6_amber.frcmod
> >
> >
> > protein = loadPdb "Combined_nolig.pdb"
> > complex = combine {protein ligA ligB}
> > protein = createUnit Combined_nolig.pdb
> > setBox protein "vdw"
> > solvateBox protein TIP3PBOX 14.0 iso
> > addIonsRand complex Na+ 0
> > saveamberparm complex complex.prmtop complex.inpcrd
> > quit
> >
> >
> > but when I try
> >
> > antechamber -i NADP_1.pdb -fi pdb -o NADP_1.mol2 -fo mol2 -c bcc -pf yes
> > -nc -3 -m 1 -at gaff2 -j 4
> >
> > it gives error
> >
> > Welcome to antechamber: molecular input file processor.
> >
> > acdoctor mode is on: check and diagnosis problems in the input file.
> > -- Check Format for pdb File --
> > Status: pass
> > -- Check Unusual Elements --
> > Status: pass
> > -- Check Open Valences --
> > Status: pass
> > -- Check Geometry --
> > for those bonded
> > for those not bonded
> > Status: pass
> > -- Check Weird Bonds --
> > Status: pass
> > -- Check Number of Units --
> > Status: pass
> > acdoctor mode has completed checking the input file.
> >
> > Info: Bond types are assigned for valence state (1) with penalty (1).
> > Info: Total number of electrons: 384; net charge: -3
> >
> > Running: /home/srania/Amber/amber16/bin/sqm -O -i sqm.in -o sqm.out
> > /home/srania/Amber/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
> > Cannot properly run "/home/srania/Amber/amber16/bin/sqm -O -i sqm.in -o
> > sqm.out".
> >
> > How can I solve this error
> > How can I calculate the parameters for NADP+ if I want to learn at my
> own
> >
> >
> > will be really thankful for answer
> >
> > thank you
> > Sadaf
> >
> >
> > On Sun, Jun 23, 2019 at 4:57 AM Elvis Martis <elvis.martis.bcp.edu.in>
> > wrote:
> >
> > > Hello
> > > NADP parameters are already available
> > > http://research.bmh.manchester.ac.uk/bryce/amber/.
> > >
> > >
> > > Best Regards
> > >
> > > Elvis Martis
> > >
> > >
> > >
> > > ________________________________
> > > From: Sadaf Rani <sadafrani6.gmail.com>
> > > Sent: 22 June 2019 18:56
> > > To: AMBER Mailing List
> > > Subject: [AMBER] open valance problem
> > >
> > > Dear Amber
> > > I am trying to find to parameters for co-factor NADP+ by antechamber
> > > But when I use this command:-
> > > antechamber -i NADP_noH.mol2 -fi mol2 -o NADP_amber.mol2 -fo mol2 -c
> bcc
> > > -pf yes -nc -3 -at gaff2 -j 4
> > >
> > > It gives me this error
> > >
> > > Welcome to antechamber: molecular input file processor.
> > >
> > > acdoctor mode is on: check and diagnosis problems in the input file.
> > > -- Check Format for mol2 File --
> > > Status: pass
> > > -- Check Unusual Elements --
> > > Status: pass
> > > -- Check Open Valences --
> > > Warning: The number of bonds (1) for atom (ID: 33, Name: O1N) does not
> > > match
> > > the connectivity (2) for atom type (O.3) defined in
> > > CORR_NAME_TYPE.DAT.
> > > Warning: The number of bonds (1) for atom (ID: 34, Name: O1X) does not
> > > match
> > > the connectivity (2) for atom type (O.3) defined in
> > > CORR_NAME_TYPE.DAT.
> > > Warning: The number of bonds (1) for atom (ID: 39, Name: O2A) does not
> > > match
> > > the connectivity (2) for atom type (O.3) defined in
> > > CORR_NAME_TYPE.DAT.
> > > Warning: The number of bonds (1) for atom (ID: 43, Name: O2X) does not
> > > match
> > > the connectivity (2) for atom type (O.3) defined in
> > > CORR_NAME_TYPE.DAT.
> > > Warning: The number of bonds (3) for atom (ID: 55, Name: C4N) does not
> > > match
> > > the connectivity (4) for atom type (C.3) defined in
> > > CORR_NAME_TYPE.DAT.
> > > Warning: The number of bonds (3) for atom (ID: 72, Name: N9A) does not
> > > match
> > > the connectivity (2) for atom type (N.ar) defined in
> > > CORR_NAME_TYPE.DAT.
> > > But, you may safely ignore the warnings if your molecule
> > > uses atom names or element names as atom types.
> > > -- Check Geometry --
> > > for those bonded
> > > for those not bonded
> > > Status: pass
> > > -- Check Weird Bonds --
> > > /home/srania/Amber/amber16/bin/to_be_dispatched/antechamber: Fatal
> Error!
> > > Weird atomic valence (3) for atom (ID: 55, Name: C4N).
> > > Possible open valence.
> > >
> > > Hoe to solve this issue
> > > I have attached .mol2 file if there is something wrong please tell me.
> > >
> > > thank you in advance
> > > _______________________________________________
> > > 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
> >
> _______________________________________________
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>
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Received on Wed Jun 26 2019 - 22:30:02 PDT
