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
>
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Received on Mon Jun 24 2019 - 22:30:02 PDT
