I suspect there were messages about missing and extra atoms for loadpdb,
and that adding these up would lead to the conclusion that your H atoms
are misnamed in the pdb.
Bill
On 9/13/16 10:29 PM, shahab shariati wrote:
> Dear Samuel,
>
> Thanks for your answer. My previous problem (cannot run
> "/share/apps/amber/amber14/bin/sqm
> -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit) was solved.
>
> Now, I have another problem. For my protein structure, I used following
> commands:
>
> $AMBERHOME/exe/reduce pr_h.pdb > pr.pdb
>
> tleap -f pr.in
>
> pr.in file is as follows:
>
> source leaprc.ff99SB
>
> pr = loadpdb pr.pdb
>
> set default PBRadii mbondi2
>
> saveamberparm pr pr.prmtop pr.inpcrd
>
> quit
>
> ---------------------------------------------------------
> But, I encountered with:
>
> FATAL: Atom .R<CLEU 124>.A<H04 25> does not have a type.
> FATAL: Atom .R<CLEU 124>.A<H05 26> does not have a type.
> FATAL: Atom .R<CLEU 124>.A<H06 27> does not have a type.
> FATAL: Atom .R<CLEU 124>.A<H07 28> does not have a type.
> FATAL: Atom .R<CLEU 124>.A<H08 29> does not have a type.
> FATAL: Atom .R<CLEU 124>.A<H09 30> does not have a type.
> FATAL: Atom .R<CLEU 124>.A<H10 31> does not have a type.
> FATAL: Atom .R<CLEU 124>.A<H11 32> does not have a type.
> FATAL: Atom .R<CLEU 124>.A<H12 33> does not have a type.
> FATAL: Atom .R<CLEU 124>.A<H13 34> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
>
> There is this error for most of the Hydrogen atoms.
>
> How to resolve this problem?
> _______________________________________________
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Received on Wed Sep 14 2016 - 00:00:02 PDT
