AMBER Archive (2009)

Subject: Re: [AMBER] Trouble saving amberparm files

From: Tom Joseph (ttjoseph_at_gmail.com)
Date: Mon Jul 13 2009 - 16:14:39 CDT

That is to say, delete all the hydrogens just to be safe.

--Tom

On Mon, Jul 13, 2009 at 5:13 PM, Tom Joseph<ttjoseph_at_gmail.com> wrote:
> Ah, I should have looked more closely. It seems like the names of your
> hydrogens (HN, HB1, HG1, etc.) do not match those in ff99, which is
> why leap doesn't know what to do with them. You should be able to
> delete them from the PDB file and leap will automatically add them
> back again with the correct names.
>
> (You may also wish to reconsider using ff99 to begin with; it has been
> deprecated. ff99SB is a better choice.)
>
> --Tom
>
> On Mon, Jul 13, 2009 at 5:06 PM, Alison
> Saunders<alison.m.saunders_at_gmail.com> wrote:
>> I did specify a force field: ff99.
>>
>> On Mon, Jul 13, 2009 at 1:16 PM, Tom Joseph <ttjoseph_at_gmail.com> wrote:
>>
>>> Did you specify a force field when invoking leap?
>>>
>>> --Tom
>>>
>>> > Hello,
>>> >
>>> > Here is part of my pdb file:
>>> - snip! -
>>> >
>>> >
>>> > I added Na+ ions in xleap to neautralize it, and I used solvatebox to put
>>> it
>>> > in water. My trouble comes when I try to saveamberparm. I get the errors:
>>> >
>>> >
>>> >
>>> > FATAL:  Atom .R<NMET 0>.A<HN 20> does not have a type.
>>> > FATAL:  Atom .R<NMET 0>.A<HB1 21> does not have a type.
>>> > FATAL:  Atom .R<NMET 0>.A<HG1 22> does not have a type.
>>> > FATAL:  Atom .R<GLN 1>.A<HN 18> does not have a type.
>>> > FATAL:  Atom .R<GLN 1>.A<HB1 19> does not have a type.
>>> > FATAL:  Atom .R<GLN 1>.A<HG1 20> does not have a type.
>>> > FATAL:  Atom .R<ALA 2>.A<HN 11> does not have a type.
>>> > FATAL:  Atom .R<MET 3>.A<HN 18> does not have a type.
>>> > FATAL:  Atom .R<MET 3>.A<HB1 19> does not have a type.
>>> > FATAL:  Atom .R<MET 3>.A<HG1 20> does not have a type.
>>> > FATAL:  Atom .R<ILE 4>.A<HN 20> does not have a type.
>>> > FATAL:  Atom .R<ILE 4>.A<HG11 21> does not have a type.
>>> > FATAL:  Atom .R<ALA 5>.A<HN 11> does not have a type.
>>> > FATAL:  Atom .R<VAL 6>.A<HN 17> does not have a type.
>>> > FATAL:  Atom .R<ALA 7>.A<HN 11> does not have a type.
>>> > FATAL:  Atom .R<SER 8>.A<HN 12> does not have a type.
>>> > FATAL:  Atom .R<SER 8>.A<HB1 13> does not have a type.
>>> > FATAL:  Atom .R<GLN 9>.A<HN 18> does not have a type.
>>> > FATAL:  Atom .R<GLN 9>.A<HB1 19> does not have a type.
>>> > FATAL:  Atom .R<GLN 9>.A<HG1 20> does not have a type.
>>> > FATAL:  Atom .R<ILE 10>.A<HN 20> does not have a type.
>>> > FATAL:  Atom .R<ILE 10>.A<HG11 21> does not have a type.
>>> > FATAL:  Atom .R<SER 11>.A<HN 12> does not have a type.
>>> > FATAL:  Atom .R<SER 11>.A<HB1 13> does not have a type.
>>> > FATAL:  Atom .R<PRO 12>.A<HB1 15> does not have a type.
>>> >
>>> > etc. etc.
>>> >
>>> > Any ideas on how to fix this problem?
>>> >
>>> > Thanks!
>>> > Alison Saunders
>>> > _______________________________________________
>>> > AMBER mailing list
>>> > AMBER_at_ambermd.org
>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>> >
>>>
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