AMBER Archive (2009)

Subject: Re: [AMBER] xleap problem

From: oguz gurbulak (gurbulakoguz_at_yahoo.com)
Date: Sun Jan 25 2009 - 10:02:50 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

--- On Sun, 1/25/09, David A. Case <case_at_biomaps.rutgers.edu> wrote:

From: David A. Case <case_at_biomaps.rutgers.edu>
Subject: Re: [AMBER] xleap problem
To: "AMBER Mailing List" <amber_at_ambermd.org>
Date: Sunday, January 25, 2009, 7:57 AM

On Sun, Jan 25, 2009, oguz gurbulak wrote:

> I?m trying to get the prmtop and inpcrd files for my n-alkanes
> simulations with using xleap. My leap.log file is in below. I want to
> do MD simulations for 100 n-dodecane †molecules. I attached the related
> files to the mail. I used packmol in order to get my pdb file that
> includes 100 n-dodecane †molecules. Then I started the minimization, but
> the min. progress stopped and I got an empty min.out file. I thought
> that I couldn?t get the prmtop and inpcrd files †succesfully. Could you
> please help me to solve this problem and get prmtop and inpcrd files
> succesfully with xleap ?

If you try to run sander and get an empty min.out file, that probably
has nothing to do with whether you are running dodecane or something
else, or with the nature of your prmtop and inpcrd files.

Run a simple sander minimization from the tutorials, so that you have a
working example. Then change substitute your prmtop and inpcrd file and
run again. Try to localize the differences between what works and what
fails.

I don't think anyone on the list can help much right now: your problem is
with the minmization step, but the only information you provided in your
email was about the LEaP part. That is: you provided lots of information
about the things that (apparently) worked fine, but no information about
the step that failed.

...dac

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