Dear Amber community,
I have been having some problems with processing pdb files (created by SYBYL Tripos) in xLEAP.
I am attaching a SYBYL pdb file (nea.pdb) for neamine (an aminoglycoside) for amber experts to see.
I would like to create prmtop and nea.x files for neamine in LEAP using leaprc.glycam04. Oh by the way! leaprc.glycam04EP seems to have some problems with recognizing specific terms in glycam04EP.dat file. Because someoneelse has already E-Mailed us today about the same problem with leaprc.glycam04EP, I will not reiterate things. Hence, I will only wait to see if experts can troubleshoot the glycam04EP problem.
Anyway..! My problem is that LEAP fails to creat and save parameters for neamine. It seems to me that (I think!) SYBYL pdb file formats somewhat can not be converted to AMBER pdb file formats in LEAP.
I will appreciate it very much if anyone tells me how I could modify my SYBYL pdb file in a way that xLEAP likes so that I won't have problems creating necessay prmtop and nea.x files. (Please also see a list of things that I did at the end of this E-Mail to create prmtop and nea.x parameters and a subsequent error message).
Secondly, neamine has 4 amino groups with different pKa values. Is it possible to tell LEAP or SANDER to adjust charges at a certain pH value for the amino groups by entering their pKa values? If so, how?
Best regards,
Cenk A. Andac
Faculty candidate
School of Pharmacy
Gazi University-Ankara, Turkey
cenk_andac.yahoo.com
***********************************************************************************
>source leaprc.glycam04
----- Source: /home/jenk/amber8/dat/leap/cmd/leaprc.glycam04
----- Source of /home/jenk/amber8/dat/leap/cmd/leaprc.glycam04 done
Loading parameters: /home/jenk/amber8/dat/leap/parm/glycam04.dat
Loading Prep file: /home/jenk/amber8/dat/leap/prep/glycam04.in
***********************************************************************************
> nea33 = loadpdb /home/jenk/nea/33/nea.pdb
Loading PDB file: /home/jenk/nea/33/nea.pdb
Unknown residue: BDG number: 0 type: Terminal/beginning
...relaxing end constraints to try for a dbase match
-no luck
Unknown residue: NEB number: 1 type: Terminal/last
...relaxing end constraints to try for a dbase match
-no luck
Creating new UNIT for residue: BDG sequence: 1
Created a new atom named: C5 within residue: .R<BDG 1>
Created a new atom named: C within residue: .R<BDG 1>
Created a new atom named: C4 within residue: .R<BDG 1>
Created a new atom named: O4 within residue: .R<BDG 1>
Created a new atom named: HO4 within residue: .R<BDG 1>
Created a new atom named: H4 within residue: .R<BDG 1>
Created a new atom named: C3 within residue: .R<BDG 1>
Created a new atom named: O3 within residue: .R<BDG 1>
Created a new atom named: HO3 within residue: .R<BDG 1>
Created a new atom named: H3 within residue: .R<BDG 1>
Created a new atom named: C2 within residue: .R<BDG 1>
Created a new atom named: N2 within residue: .R<BDG 1>
Created a new atom named: H23 within residue: .R<BDG 1>
Created a new atom named: H21 within residue: .R<BDG 1>
Created a new atom named: H22 within residue: .R<BDG 1>
Created a new atom named: H2 within residue: .R<BDG 1>
Created a new atom named: C1 within residue: .R<BDG 1>
Created a new atom named: H1 within residue: .R<BDG 1>
Created a new atom named: O within residue: .R<BDG 1>
Created a new atom named: HC within residue: .R<BDG 1>
Created a new atom named: H51 within residue: .R<BDG 1>
Created a new atom named: H52 within residue: .R<BDG 1>
Created a new atom named: N6 within residue: .R<BDG 1>
Created a new atom named: H63 within residue: .R<BDG 1>
Created a new atom named: H61 within residue: .R<BDG 1>
Created a new atom named: H62 within residue: .R<BDG 1>
Creating new UNIT for residue: NEB sequence: 2
Created a new atom named: C1 within residue: .R<NEB 2>
Created a new atom named: N1 within residue: .R<NEB 2>
Created a new atom named: H11 within residue: .R<NEB 2>
Created a new atom named: H12 within residue: .R<NEB 2>
Created a new atom named: H13 within residue: .R<NEB 2>
Created a new atom named: C2 within residue: .R<NEB 2>
Created a new atom named: H21 within residue: .R<NEB 2>
Created a new atom named: H22 within residue: .R<NEB 2>
Created a new atom named: C3 within residue: .R<NEB 2>
Created a new atom named: N3 within residue: .R<NEB 2>
Created a new atom named: H8 within residue: .R<NEB 2>
Created a new atom named: H31 within residue: .R<NEB 2>
Created a new atom named: H32 within residue: .R<NEB 2>
Created a new atom named: H3 within residue: .R<NEB 2>
Created a new atom named: C4 within residue: .R<NEB 2>
Created a new atom named: O4 within residue: .R<NEB 2>
Created a new atom named: H4 within residue: .R<NEB 2>
Created a new atom named: C5 within residue: .R<NEB 2>
Created a new atom named: O5 within residue: .R<NEB 2>
Created a new atom named: H7 within residue: .R<NEB 2>
Created a new atom named: H5 within residue: .R<NEB 2>
Created a new atom named: C6 within residue: .R<NEB 2>
Created a new atom named: O6 within residue: .R<NEB 2>
Created a new atom named: HO6 within residue: .R<NEB 2>
Created a new atom named: H6 within residue: .R<NEB 2>
Created a new atom named: H1 within residue: .R<NEB 2>
total atoms in file: 52
The file contained 52 atoms not in residue templates
*******************************************************************************
>saveamberparm nea33 prmtop nea33.x
Checking Unit.
FATAL: Atom .R<BDG 1>.A<C5 1> does not have a type.
FATAL: Atom .R<BDG 1>.A<C 2> does not have a type.
FATAL: Atom .R<BDG 1>.A<C4 3> does not have a type.
FATAL: Atom .R<BDG 1>.A<O4 4> does not have a type.
FATAL: Atom .R<BDG 1>.A<HO4 5> does not have a type.
FATAL: Atom .R<BDG 1>.A<H4 6> does not have a type.
FATAL: Atom .R<BDG 1>.A<C3 7> does not have a type.
FATAL: Atom .R<BDG 1>.A<O3 8> does not have a type.
FATAL: Atom .R<BDG 1>.A<HO3 9> does not have a type.
FATAL: Atom .R<BDG 1>.A<H3 10> does not have a type.
FATAL: Atom .R<BDG 1>.A<C2 11> does not have a type.
FATAL: Atom .R<BDG 1>.A<N2 12> does not have a type.
FATAL: Atom .R<BDG 1>.A<H23 13> does not have a type.
FATAL: Atom .R<BDG 1>.A<H21 14> does not have a type.
FATAL: Atom .R<BDG 1>.A<H22 15> does not have a type.
FATAL: Atom .R<BDG 1>.A<H2 16> does not have a type.
FATAL: Atom .R<BDG 1>.A<C1 17> does not have a type.
FATAL: Atom .R<BDG 1>.A<H1 18> does not have a type.
FATAL: Atom .R<BDG 1>.A<O 19> does not have a type.
FATAL: Atom .R<BDG 1>.A<HC 20> does not have a type.
FATAL: Atom .R<BDG 1>.A<H51 21> does not have a type.
FATAL: Atom .R<BDG 1>.A<H52 22> does not have a type.
FATAL: Atom .R<BDG 1>.A<N6 23> does not have a type.
FATAL: Atom .R<BDG 1>.A<H63 24> does not have a type.
FATAL: Atom .R<BDG 1>.A<H61 25> does not have a type.
FATAL: Atom .R<BDG 1>.A<H62 26> does not have a type.
FATAL: Atom .R<NEB 2>.A<C1 1> does not have a type.
FATAL: Atom .R<NEB 2>.A<N1 2> does not have a type.
FATAL: Atom .R<NEB 2>.A<H11 3> does not have a type.
FATAL: Atom .R<NEB 2>.A<H12 4> does not have a type.
FATAL: Atom .R<NEB 2>.A<H13 5> does not have a type.
FATAL: Atom .R<NEB 2>.A<C2 6> does not have a type.
FATAL: Atom .R<NEB 2>.A<H21 7> does not have a type.
FATAL: Atom .R<NEB 2>.A<H22 8> does not have a type.
FATAL: Atom .R<NEB 2>.A<C3 9> does not have a type.
FATAL: Atom .R<NEB 2>.A<N3 10> does not have a type.
FATAL: Atom .R<NEB 2>.A<H8 11> does not have a type.
FATAL: Atom .R<NEB 2>.A<H31 12> does not have a type.
FATAL: Atom .R<NEB 2>.A<H32 13> does not have a type.
FATAL: Atom .R<NEB 2>.A<H3 14> does not have a type.
FATAL: Atom .R<NEB 2>.A<C4 15> does not have a type.
FATAL: Atom .R<NEB 2>.A<O4 16> does not have a type.
FATAL: Atom .R<NEB 2>.A<H4 17> does not have a type.
FATAL: Atom .R<NEB 2>.A<C5 18> does not have a type.
FATAL: Atom .R<NEB 2>.A<O5 19> does not have a type.
FATAL: Atom .R<NEB 2>.A<H7 20> does not have a type.
FATAL: Atom .R<NEB 2>.A<H5 21> does not have a type.
FATAL: Atom .R<NEB 2>.A<C6 22> does not have a type.
FATAL: Atom .R<NEB 2>.A<O6 23> does not have a type.
FATAL: Atom .R<NEB 2>.A<HO6 24> does not have a type.
FATAL: Atom .R<NEB 2>.A<H6 25> does not have a type.
FATAL: Atom .R<NEB 2>.A<H1 26> does not have a type.
Failed to generate parameters
Parameter file was not saved.
---------------------------------
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Received on Wed Jun 30 2004 - 16:53:00 PDT
