AMBER Archive (2009)

Subject: [AMBER] xleap problem

From: oguz gurbulak (gurbulakoguz_at_gmail.com)
Date: Sun Jan 25 2009 - 10:34:39 CST

Dear David Case ,

I tried to do a tutorial and a run a minimization in TUTORƯAL A2 as you
said in order to control the min. process. And I didn't see anything wrong
in TUTORƯAL A2 min.out file . I got the same min.out file in TUTORƯAL 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
couldn't 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 can't give any information apart from that. Because that's all.
Now I'm waiting for your help. By the way I want to learn if the bold italic
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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