AMBER Archive (2007)

Subject: Re: AMBER: problems in adding ACE and NME group

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Jun 20 2007 - 10:37:45 CDT

did leap read in the ace and nme? if leap was ok with it,
sander should be fine.

On 6/20/07, backy <backy_at_ibms.sinica.edu.tw> wrote:
>
> Hi:
>
> but even I tried not to set idiel , the error messages are still there.
>
> And I worried about if the setting of ACE and NME are correct?
>
> Because the last 4 lines looks weird.
>
>
>
> backy
>
>
>
>
> ----------------------------------------------------------------------------
>
>
>
>
>
> Warning: name change in pdb file residue 1 ;
> this residue is split into ACE and ALA.
> Warning: name change in pdb file residue 149 ;
> this residue is split into HID and NME.
> 2 residues had naming warnings.
> There are split residues;
> residue sequence numbers will not correspond to those in the pdb.
> Created a new atom named: N within residue: .R<ACE 1>
> Added missing heavy atom: .R<ACE 1>.A<O 6>
> Added missing heavy atom: .R<ACE 1>.A<C 5>
> Added missing heavy atom: .R<ACE 1>.A<CH3 2>
> Added missing heavy atom: .R<ALA 2>.A<N 1>
> Added missing heavy atom: .R<HID 150>.A<NE2 13>
> Created a new atom named: NE2 within residue: .R<NME 151>
> Added missing heavy atom: .R<NME 151>.A<N 1>
> Added missing heavy atom: .R<NME 151>.A<CH3 3>
> total atoms in file: 1190
> Leap added 1153 missing atoms according to residue templates:
> 7 Heavy
> 1146 H / lone pairs
> The file contained 2 atoms not in residue templates
> Checking Unit.
> WARNING: There is a bond of 103.383324 angstroms between:
> ------- .R<ACE 1>.A<C 5> and .R<ALA 2>.A<N 1>
> WARNING: The unperturbed charge of the unit: 10.000000 is not zero.
> FATAL: Atom .R<ACE 1>.A<N 7> does not have a type.
> FATAL: Atom .R<NME 151>.A<NE2 7> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
> Quit
>
>
> ---------------------------------------------------------------------------
>
>
>
>
> ----- Original Message -----
> *From:* Carlos Simmerling <carlos.simmerling_at_gmail.com>
> *To:* amber_at_scripps.edu
> *Sent:* Wednesday, June 20, 2007 7:28 PM
> *Subject:* Re: AMBER: problems in adding ACE and NME group
>
> one of your namelist variables is wrong, usually it is easiest
> to find this by removing them one by one until it runs, then you
> know which one was incorrect. in this case it might be that idiel is not
> a sander variable.
>
>
> On 6/20/07, backy <backy_at_ibms.sinica.edu.tw> wrote:
> >
> > Dear Amber users:
> >
> > I am using amber 9 and want to cap the N and C terminal for the given
> > protein.
> > So, in the given protein the first residue at position 1 and the last
> > one at
> > position 149 were modified by adding ACE and NME groups.
> >
> >
> > ATOM 1 C ACE A 1 70.110 65.868 39.946 1.00 0.00
> > ATOM 2 CA ALA A 1 70.537 66.473 38.657 1.00 0.00
> > ATOM 3 C ALA A 1 69.639 67.664 38.316 1.00 0.00
> > ATOM 4 O ALA A 1 68.434 67.654 38.604 1.00 0.00
> > ATOM 5 CB ALA A 1 70.456 65.436 37.551 1.00 0.00
> > ATOM 6 N THR A 2 70.232 68.687 37.711 1.00 0.00
> > ATOM 7 CA THR A 2 69.495 69.875 37.320 1.00 0.00
> > ATOM 8 C THR A 2 69.540 70.004 35.797 1.00 0.00
> > .
> >
> > .
> >
> > .
> >
> > ATOM 1182 CA HID A 149 72.111 68.499 32.373 1.00 0.00
> > ATOM 1183 C HID A 149 73.534 68.060 32.700 1.00 0.00
> > ATOM 1184 O HID A 149 74.355 67.976 31.762 1.00 0.00
> > ATOM 1185 CB HID A 149 71.171 67.340 32.690 1.00 0.00
> > ATOM 1186 CG HID A 149 71.681 66.008 32.234 1.00 0.00
> > ATOM 1187 ND1 HID A 149 71.796 65.669 30.903 1.00 0.00
> > ATOM 1188 CD2 HID A 149 72.104 64.928 32.935 1.00 0.00
> > ATOM 1189 CE1 HID A 149 72.263 64.437 30.803 1.00 0.00
> > ATOM 1190 N NME A 149 72.457 63.965 32.021 1.00 0.00
> >
> >
> > Also, here below is the input file, sander.in_leo, for ironing out the
> > poor
> > placemats of these two gropes.
> >
> >
> >
> > min + md
> > &cntrl imin = 1, irest=0, ibelly=1,
> > ntx=1, idiel = 0, cut = 8.0, SCEE=1.2,
> > ntpr=500, maxcyc=20000, ncyc=8000, drms=0.01
> > &end
> > Group input for restrained atoms
> > 50.0
> > RES 1
> > RES 151
> > END
> > END
> >
> >
> >
> >
> > Finally, here comes the error messages like this:
> >
> > forrtl: severe (19): invalid reference to variable in NAMELIST input,
> > unit
> > 5, file
> > /mount/disk15/backy/system/RNA/Amber/RNA_bound/Backy/cap-1jbs-A-GB/sander.in_leo,
> >
> > line 3, position 14
> > Image PC Routine Line Source
> > sander 08560280 Unknown Unknown Unknown
> > sander 0855FD78 Unknown Unknown Unknown
> > sander 0852D0D9 Unknown Unknown Unknown
> > sander 084F098C Unknown Unknown Unknown
> > sander 084F0E2F Unknown Unknown Unknown
> > sander 0850E440 Unknown Unknown Unknown
> > sander 080E96B2 Unknown Unknown Unknown
> > sander 080D040C Unknown Unknown Unknown
> > sander 080D0155 Unknown Unknown Unknown
> > sander 0804A5E8 Unknown Unknown Unknown
> > Unknown 006BBDE3 Unknown Unknown Unknown
> > sander 0804A4A1 Unknown Unknown Unknown
> >
> >
> >
> >
> > Could anyone figure what's wrong?
> >
> > Thanks.
> >
> >
> >
> >
> >
> > backy
> >
> >
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
>
>
> ------------------------------
>
> No virus found in this incoming message.
> Checked by AVG Free Edition.
> Version: 7.5.472 / Virus Database: 269.9.1/854 - Release Date: 2007/6/19
> $U$H 01:12
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu