Thanks. I downloaded the project files and generated the mol2 and .off
files. I loaded the .off file using loadoff. Now I can see FAD in the
list. But when I load the pdb file of FAD, i get
> fad = loadpdb FAD.pdb
Loading PDB file: ./FAD.pdb
Created a new atom named: P within residue: .R<B5 904>
Created a new atom named: PA within residue: .R<B5 904>
Created a new atom named: O1P within residue: .R<B5 904>
Created a new atom named: O2P within residue: .R<B5 904>
Created a new atom named: O3P within residue: .R<B5 904>
Created a new atom named: O5' within residue: .R<B5 904>
Created a new atom named: C1B within residue: .R<B5 904>
Created a new atom named: N1A within residue: .R<B5 904>
Created a new atom named: O1A within residue: .R<B5 904>
Created a new atom named: C2A within residue: .R<B5 904>
Created a new atom named: C2B within residue: .R<B5 904>
Created a new atom named: O2 within residue: .R<B5 904>
Created a new atom named: O2A within residue: .R<B5 904>
Created a new atom named: O2B within residue: .R<B5 904>
Created a new atom named: C3B within residue: .R<B5 904>
Created a new atom named: N3A within residue: .R<B5 904>
Created a new atom named: O3B within residue: .R<B5 904>
Created a new atom named: C4A within residue: .R<B5 904>
Created a new atom named: C4B within residue: .R<B5 904>
Created a new atom named: C4X within residue: .R<B5 904>
Created a new atom named: O4 within residue: .R<B5 904>
Created a new atom named: O4B within residue: .R<B5 904>
Created a new atom named: C5A within residue: .R<B5 904>
Created a new atom named: C5B within residue: .R<B5 904>
Created a new atom named: C5X within residue: .R<B5 904>
Created a new atom named: N5 within residue: .R<B5 904>
Created a new atom named: O5B within residue: .R<B5 904>
Created a new atom named: C6A within residue: .R<B5 904>
Created a new atom named: N6A within residue: .R<B5 904>
Created a new atom named: C7 within residue: .R<B5 904>
Created a new atom named: C7M within residue: .R<B5 904>
Created a new atom named: N7A within residue: .R<B5 904>
Created a new atom named: C8A within residue: .R<B5 904>
Created a new atom named: C8M within residue: .R<B5 904>
Created a new atom named: C9 within residue: .R<B5 904>
Created a new atom named: C9A within residue: .R<B5 904>
Created a new atom named: N9A within residue: .R<B5 904>
Created a new atom named: C10 within residue: .R<B5 904>
Created a new atom named: N10 within residue: .R<B5 904>
Added missing heavy atom: .R<B5 904>.A<N9 25>
Added missing heavy atom: .R<POP 905>.A<O5A 1>
Added missing heavy atom: .R<POP 905>.A<PA 2>
Added missing heavy atom: .R<POP 905>.A<OA1 3>
Added missing heavy atom: .R<POP 905>.A<OA2 4>
Added missing heavy atom: .R<POP 905>.A<OP 5>
Added missing heavy atom: .R<POP 905>.A<PB 6>
Added missing heavy atom: .R<POP 905>.A<OB1 7>
Added missing heavy atom: .R<POP 905>.A<OB2 8>
Added missing heavy atom: .R<POP 905>.A<O5B 9>
Added missing heavy atom: .R<LNK 906>.A<C5 16>
Added missing heavy atom: .R<LNK 906>.A<C4 12>
Added missing heavy atom: .R<LNK 906>.A<O4 14>
Added missing heavy atom: .R<LNK 906>.A<C3 8>
Added missing heavy atom: .R<LNK 906>.A<O3 10>
Added missing heavy atom: .R<LNK 906>.A<C2 4>
Added missing heavy atom: .R<LNK 906>.A<O2 6>
Added missing heavy atom: .R<LNK 906>.A<C1 1>
Added missing heavy atom: .R<FLO 907>.A<N10 8>
Added missing heavy atom: .R<FLO 907>.A<C10A 9>
Added missing heavy atom: .R<FLO 907>.A<C9A 13>
Added missing heavy atom: .R<FLO 907>.A<C4A 10>
Added missing heavy atom: .R<FLO 907>.A<N1 1>
Added missing heavy atom: .R<FLO 907>.A<C9 14>
Added missing heavy atom: .R<FLO 907>.A<C5A 12>
Added missing heavy atom: .R<FLO 907>.A<N5 11>
Added missing heavy atom: .R<FLO 907>.A<C4 6>
Added missing heavy atom: .R<FLO 907>.A<C2 2>
Added missing heavy atom: .R<FLO 907>.A<C8 16>
Added missing heavy atom: .R<FLO 907>.A<C6 18>
Added missing heavy atom: .R<FLO 907>.A<O4 7>
Added missing heavy atom: .R<FLO 907>.A<N3 4>
Added missing heavy atom: .R<FLO 907>.A<O2 3>
Added missing heavy atom: .R<FLO 907>.A<C7 17>
Added missing heavy atom: .R<FLO 907>.A<C8M 24>
Added missing heavy atom: .R<FLO 907>.A<C7M 20>
Added missing heavy atom: .R<B5 904>.A<C5 21>
Added missing heavy atom: .R<B5 904>.A<N6 17>
Added missing heavy atom: .R<B5 904>.A<N7 22>
total atoms in file: 53
Leap added 70 missing atoms according to residue templates:
39 Heavy
31 H / lone pairs
The file contained 39 atoms not in residue templates
Check fad gives
FATAL: Atom .R<B5 904>.A<P 31> does not have a type.
FATAL: Atom .R<B5 904>.A<PA 32> does not have a type.
FATAL: Atom .R<B5 904>.A<O1P 33> does not have a type.
FATAL: Atom .R<B5 904>.A<O2P 34> does not have a type.
FATAL: Atom .R<B5 904>.A<O3P 35> does not have a type.
FATAL: Atom .R<B5 904>.A<O5' 36> does not have a type.
FATAL: Atom .R<B5 904>.A<C1B 37> does not have a type.
FATAL: Atom .R<B5 904>.A<N1A 38> does not have a type.
FATAL: Atom .R<B5 904>.A<O1A 39> does not have a type.
FATAL: Atom .R<B5 904>.A<C2A 40> does not have a type.
FATAL: Atom .R<B5 904>.A<C2B 41> does not have a type.
FATAL: Atom .R<B5 904>.A<O2 42> does not have a type.
FATAL: Atom .R<B5 904>.A<O2A 43> does not have a type.
FATAL: Atom .R<B5 904>.A<O2B 44> does not have a type.
FATAL: Atom .R<B5 904>.A<C3B 45> does not have a type.
FATAL: Atom .R<B5 904>.A<N3A 46> does not have a type.
FATAL: Atom .R<B5 904>.A<O3B 47> does not have a type.
FATAL: Atom .R<B5 904>.A<C4A 48> does not have a type.
FATAL: Atom .R<B5 904>.A<C4B 49> does not have a type.
FATAL: Atom .R<B5 904>.A<C4X 50> does not have a type.
FATAL: Atom .R<B5 904>.A<O4 51> does not have a type.
FATAL: Atom .R<B5 904>.A<O4B 52> does not have a type.
FATAL: Atom .R<B5 904>.A<C5A 53> does not have a type.
FATAL: Atom .R<B5 904>.A<C5B 54> does not have a type.
FATAL: Atom .R<B5 904>.A<C5X 55> does not have a type.
FATAL: Atom .R<B5 904>.A<N5 56> does not have a type.
FATAL: Atom .R<B5 904>.A<O5B 57> does not have a type.
FATAL: Atom .R<B5 904>.A<C6A 58> does not have a type.
FATAL: Atom .R<B5 904>.A<N6A 59> does not have a type.
FATAL: Atom .R<B5 904>.A<C7 60> does not have a type.
FATAL: Atom .R<B5 904>.A<C7M 61> does not have a type.
FATAL: Atom .R<B5 904>.A<N7A 62> does not have a type.
FATAL: Atom .R<B5 904>.A<C8A 63> does not have a type.
FATAL: Atom .R<B5 904>.A<C8M 64> does not have a type.
FATAL: Atom .R<B5 904>.A<C9 65> does not have a type.
FATAL: Atom .R<B5 904>.A<C9A 66> does not have a type.
FATAL: Atom .R<B5 904>.A<N9A 67> does not have a type.
FATAL: Atom .R<B5 904>.A<C10 68> does not have a type.
FATAL: Atom .R<B5 904>.A<N10 69> does not have a type.
I would be really thankful for any help.
Regards.
On 2014-05-01 19:07, ABEL Stephane 175950 wrote:
> Hello,
>
> These parameters are available here in RED.DB
>
> http://q4md-forcefieldtools.org/REDDB/projects/F-90/ [1]
> http://q4md-forcefieldtools.org/REDDB/projects/F-91/ [2]
>
> Regards
>
> --------------------------------------------------------------------
> Stéphane Abel, Ph.D.
> CEA Saclay DSV/IbItec-S/SB2SM & CNRS UMR 8221
> Bat 528, Office 138C
> Gif-sur-Yvette, F-91191 FRANCE
> Phone (portable) : +33 6 49 37 70 60
> ________________________________________
> De : amin.imtech.res.in [amin.imtech.res.in]
> Envoyé : jeudi 1 mai 2014 15:26
> À : amber.ambermd.org
> Objet : [AMBER] Parameters for FAD
>
> Dear Amber users and Dr. Francois
>
> I am going to do some simulations of a protein which has FAD bound to
> it. I was looking for the parameters of FAD and found the post
> http://archive.ambermd.org/200812/0328.html [3]. These are exactly the
> parameters I was looking for. Can you please share with me the
> parameters for
>
> 2008-10-19 23:10 FAD.mol2
> 2008-10-19 23:10 FADH.mol2
> 2008-10-19 23:10 FADHP1.mol2
> 2008-10-19 23:10 FADHP2.mol2
> 2008-10-19 23:10 FADP1.mol2
> 2008-10-19 23:10 FADP2.mol2
>
> I would be really thankful for your help.
>
> Regards.
>
> Amin.
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber [4]
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber [4]
Links:
------
[1]
http://q4md-forcefieldtools.org/REDDB/projects/F-90/
[2]
http://q4md-forcefieldtools.org/REDDB/projects/F-91/
[3]
http://archive.ambermd.org/200812/0328.html
[4]
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
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Received on Thu May 01 2014 - 12:30:02 PDT
