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
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jun 24 2019 - 13:30:02 PDT
