AMBER Archive (2009)

Subject: Re: [AMBER] Atom names

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Jun 02 2009 - 06:39:25 CDT

when I look at the PD_PDB.pdb file in vmd the bonds are not right, so you
might want to fix that before loading it into leap. I don't think this is an
Amber problem. where did you get that pdb file?

On Tue, Jun 2, 2009 at 6:53 AM, Rose Tamil <rosetamil26_at_googlemail.com>wrote:

> 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
> command.
>
> "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 setup.in
> 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.
> regards,
> Anitha
>
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