AMBER Archive (2005)

Subject: Re: AMBER: An atom name with 4 characters is not compatible with Leap ?

From: ivan_at_mmb.pcb.ub.es
Date: Fri Jul 22 2005 - 03:16:52 CDT

Dear Eric,

I think it's a limitation that will need a deep look at the code to be
solved ... I suspect it won't be an easy task

as far as I am concerned only "H" are allowed to have 4 characters

(amber 7 manual p.25 top info about atom names)

On the other hand, the atom name has no relevance, it is chosen
arbitrarily, e.g. if you have three CL atoms call them CL1, CL2, CL3,
that's my suggestion (or any other 3-character name)

Regards,

Ivan.

On Fri, 22 Jul 2005, Arnoult, Eric [PRDFR] wrote:

> Dear All,
>
> I prepare the "prep" file for several ligands with antechamber.
> When the ligand contains an halogen atom (CL for example), the atom name for
> this halogen atom is wrote with 4 characters.
>
> Then, I load this "prep" file in Leap. An atom name with 4 characters seems
> to be not compatible with Leap because I obtained an error message :
> "FATAL: Atom .R<lig 276>.A<CL2> does not have type"
>
> If I edit the "prep" file and modify the atom name from CL29 to CL2, I
> successfully pass this step.
> Is it a bug or limitation ? What should I do ? Did somebody modify the
> antechamber's code or leap's code for this problem ?
>
>
>
> Many Thanks
>
>
> Best regards
>
> Eric ARNOULT
>
>
>
> my prep.in :
> 0 0 2
>
> This is a remark line
>
> molecule.res
>
> lig INT 0
>
> CORRECT OMIT DU BEG
>
> 0.0000
>
> 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
>
> 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
>
> 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
>
> ...
>
> 51 CL29 cl M 50 48 46 1.758 120.465 177.991 -0.04408
>
> ...
>
>
> IMPROPER
>
> ...
>
> C26 C28 C27 CL29
>
> DONE
>
>
>

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