Hi Dr.David
I am struck what to do? As antechamber is giving trouble to make mol2 files. So I have used other software to prepare mol2
I have prepared a peptide by using Leap.
Then I was trying to use antchamber
> antechamber -i PLX4720.pdb -fi pdb -o PLX4720.mol2 -fo mol2 -c bcc -s 2
But It was continuously giving me error
[axt651.pegasus test]$ antechamber -i 2.pdb -fi pdb -o p.mol2 -fo mol2 -c bcc -s 2
Running: /nethome/axt651/apps/amber14/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
---Judge bond type for Residue 1 with ID of 1 and Name of GLU ---
---Judge bond type for Residue 2 with ID of 2 and Name of ASN ---
Warning: the assigned bond types may be wrong, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase PSCUTOFF in define.h and recompile bondtype.c
Be cautious, use a large value of PSCUTOFF (>100) will significantly increase the computation time
---Judge bond type for Residue 3 with ID of 3 and Name of VAL ---
Warning: the assigned bond types may be wrong, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase PSCUTOFF in define.h and recompile bondtype.c
Be cautious, use a large value of PSCUTOFF (>100) will significantly increase the computation time
---Judge bond type for Residue 4 with ID of 4 and Name of TYR ---
Info: Bond types are assigned for valence state 15 with penalty of 4
---Judge bond type for Residue 5 with ID of 5 and Name of GLY ---
Info: Bond types are assigned for valence state 7 with penalty of 2
---Judge bond type for Residue 6 with ID of 6 and Name of PHE ---
Warning: the assigned bond types may be wrong, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase PSCUTOFF in define.h and recompile bondtype.c
Be cautious, use a large value of PSCUTOFF (>100) will significantly increase the computation time
---Judge bond type for Residue 7 with ID of 7 and Name of ASP ---
Info: Bond types are assigned for valence state 61 with penalty of 2
---Judge bond type for Residue 8 with ID of 8 and Name of MET ---
Info: Bond types are assigned for valence state 1 with penalty of 1
---Judge bond type for Residue 9 with ID of 9 and Name of SER ---
Info: Bond types are assigned for valence state 15 with penalty of 4
Running: /nethome/axt651/apps/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 490; net charge: 0
Running: /nethome/axt651/apps/amber14/bin/sqm -O -i sqm.in -o sqm.out
Error: cannot run "/nethome/axt651/apps/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
So I have used Avogardo to make mol2 file form me.
There after I have used following commands to make those files
> tleap -s -f $AMBERHOME/dat/leap/cmd/oldff/leaprc.ff99SB
> source leaprc.gaff
> PLX = loadmol2 PLX4720.mol2
> loadamberparams PLX4720.frcmod
At this stage I am getting an error
Unknown keyword: C.3-C.3-S. in parameter file. Perhaps a format error?
> saveoff PLX PLX4720.lib
> saveamberparm PLX PLX4720.prmtop PLX4720.inpcrd
> quit
I am struck what to do? As antechamber is giving trouble to make mol2 files.
Kindly suggest me what should I do.
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Wednesday, October 19, 2016 8:27:20 AM
To: AMBER Mailing List
Subject: Re: [AMBER] frcmod file error
On Wed, Oct 19, 2016, Thakur, Abhishek wrote:
>
> For your reference I am attaching my frcmod and lib file
How did you make the frcmod and lib files? It looks like you are using Sybyl
atom types. These won't work in Amber: you will need to use either gaff or
Amber atom types.
....dac
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Received on Wed Oct 19 2016 - 14:30:02 PDT
