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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Received on Tue Jun 25 2019 - 22:00:02 PDT
