AMBER Archive (2008)

Subject: Re: AMBER: Atom names CL and four characters

From: Francesco Pietra (
Date: Fri Oct 24 2008 - 17:44:31 CDT

You are rigth, and please have my apologies. I should have waited to
post the message. In the meantime:

(1) Replaced "CL" with "Cl" in the residue for the organic molecule

(2) Reset all TER lines that Chimera had removed for the many capping groups

(3) Replaced HETATM (introduced by Chimera for the capping groups,
HIP, and the organic molecule) with ATOM

(4) Nothing else done for names

allowed to create valid prmtop/inpcrd for both the complex in a
lipidic membrane and all that in a TIP3PBOX.


On Fri, Oct 24, 2008 at 9:21 PM, David A. Case <> wrote:
> On Fri, Oct 24, 2008, Francesco Pietra wrote:
>> 1st Question: prepin/frcmod (for an organic compound containing
>> covalent chlorine), coming from Antechamber in AmberTools1.2 are not
>> accepted by leap:
>> Atom .R<AA1 ###>.A<CL ##> does not have a type.
>> I guess that leap expects "Cl" for chlorine.How to arrange so that
>> Antechamber prepares files accordingly?
> I would think that by now, you would have enough experience to tackle these
> sorts of problems yourself. There are examples in the test/antechamber area
> of molecules containing chlorine (e.g. sustiva). You can explore how what you
> are doing differs from the examples that work. (My wild guess is that you are
> confusing atom name and atom type, or that you didn't load gaff.dat into
> LEaP.)
> In any event, just citing the error message above, with no details about what
> you did, doesn't give anyone on the list a chance to help.
>> 2nd Related Question: As the protein for the above complex (coming
>> from work up with Chimera) has atom names with four
>> characters/numbers, are, for example,
>> 1C21
>> RH11
>> accepted by Amber10/AmberTools1.2, or should they be edited to
>> C211
>> H11R
>> as it was the case with Amber9?
> I'm confused here as well: why not just try the experiment and find out for
> yourself?
> ...dac
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