AMBER Archive (2009)

Subject: [AMBER] Atom names

From: Rose Tamil (
Date: Tue Jun 02 2009 - 05:53:50 CDT

Hi all,
        I try to get coordinate and topology files for Anthracene(Ant)
stacked structure. First I minimized the Ant dimer using gaussian. Then i
derived resp charges for that system using following keywords.

"#P HF/6-31G* SCF=Tight Pop=MK IOp(6/33=2) iop(6/41=2) iop(6/42=1)"

I could create prep file for one anthracene molecule (of that dimer) using

"antechamber -i PD-Resp.out -fi gout -o PD_prep.prepin -fo prepi -c resp"

I could get parm and crd files by loading the following commands.

tleap -s -f
source leaprc.ff03
loadamberparams gaff.dat
loadamberprep PD_prep.prepin
com=loadpdb PD_PDB.pdb
saveamberparm com Final.parm Final.crd
When i tried to look at the structure (by converting crd into pdb, ambpdb -p
Final.parm < Final.crd > Final.pdb), i could see all the atoms, but they are
all not as anthracene (three rings). I could see only one proper benzene
ring. Other atoms are connected in improper way. I don't know what happened.
But when i read some archives and manuals, i feel that problem is with atom
names. I think leap is not recognizing atoms in PDB files. Still i'm not
surre about the problem and how to solve it. I've attached the files here.
Does anyone have any idea or suggestions to comment on it? Any help would be
grateful. Thanks in advance.

  • application/octet-stream attachment: Final.crd

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