AMBER Archive (2009)

Subject: [AMBER] RE:xleap problem

From: oguz gurbulak (gurbulakoguz_at_yahoo.com)
Date: Sun Jan 25 2009 - 10:08:26 CST


Dear David Case ,
I tried to do a tutorial and a run a minimization in TUTOR›AL A2 †as you said in order to control the min. process. And I didnít see anything wrong in TUTOR›AL A2 †min.out file . I got the same min.out file in TUTOR›AL A2 . Before I start to use xleap for my n-dodecane simulation †I did the operations below. After all these operations I started the min. , but †I couldnít get the min.out file. I loaded gaff, a mol2 file and a pdb file and saved all of them as input files. I think I loaded all the information for min. and md simulations. I gave all the information to you about this process. I canít give any information apart from that. Because thatís all. Now Iím waiting for your help. By the way I want to learn if the red lines I signed in the process is normal or not normal to get.
Many thanks in advance.


sander -O -i min.in -o min.out -p n-dodecane.prmtop -c n-dodecane.inpcrd -r n-dodecane.rst†

1 antechamber -i n-dodecane.pdb -fi pdb -o n-dodecane_gin.gjf -fo gcrt
2 Run the gaussian ( #B3LYP/cc-pvTZ SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt )

3 antechamber -i n-dodecane_gin.out -fi gout -o c12.AA.mol2 -fo mol2 -nc 0 -c resp -at gaff -rn DEC
4 parmchk -i c12.AA.mol2 -f mol2 -o n-dodecane.frcmod †( generated empty frcmod file )
5 antechamber -i c12.AA.mol2 -fi mol2 -o n-dodecane.gaff.pdb -fo pdb
6 use packmol with n-dodecane.gaff.pdb for getting 100 molecule ( added TER cards ) n-dodecane.packmol100.pdb file
7† xleap -s -f leaprc.gaff
8 DEC = loadMol2 c12.AA.mol2
9 charge DEC
10 check DEC
11 desc DEC

UNIT name: DEC
Head atom: null
Tail atom: null
Contents:
R<DEC 1>
12 n-dodecane = loadpdb n-dodecane.packmol100.pdb
Enter zPdbReadScan from call depth† 0.
Exit† zPdbReadScan from call depth† 0.
Matching PDB residue names to LEaP variables.
(Residue 0: DEC, Terminal/last, was not found in name map.)
(Residue 1: DEC, Terminal/last, was not found in name map.)
(Residue 2: DEC, Terminal/last, was not found in name map.)
(Residue 3: DEC, Terminal/last, was not found in name map.)
(Residue 4: DEC, Terminal/last, was not found in name map.)
(Residue 5: DEC, Terminal/last, was not found in name map.)
(Residue 6: DEC, Terminal/last, was not found in name map.)
(Residue 7: DEC, Terminal/last, was not found in name map.)
(Residue 8: DEC, Terminal/last, was not found in name map.)
(Residue 9: DEC, Terminal/last, was not found in name map.)
(Residue 10: DEC, Terminal/last, was not found in name map.)
(Residue 11: DEC, Terminal/last, was not found in name map.)
.
.
.
13 saveAmberParm n-dodecane n-dodecane.prmtop n-dodecane.inpcrd
14 savepdb n-dodecane n-dodecane.leap.pdb
15 Quit

      
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