subject:"\[gmx\-users\] output pdb reformatted"

Re: [gmx-users] output pdb reformatted

2017-07-12 Thread Mark Abraham

Hi,

Please stop doing that. You're risking wasting your own time as well. ;-)

Mark

On Tue, Jul 11, 2017 at 11:52 PM Alex  wrote:

> You are absolutely right once again. I've been glancing over that topology,
> looking right at what the problem was, and not seeing it. The residue name
> column was empty, all atom types went to crap, but because I always grompp
> with -maxwarn 10 (for completely unrelated warnings in completely different
> simulations) everything seemed okay.
>
> Thanks!
>
> Alex
>
> On Tue, Jul 11, 2017 at 2:40 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 7/11/17 4:01 PM, Alex wrote:
> >
> >> Hi all,
> >>
> >> I have a tiny acetonitrile molecule here. The input pdb prior to EM is
> >> this:
> >>
> >> TITLE Gromacs Runs On Most of All Computer Systems
> >> REMARKTHIS IS A SIMULATION BOX
> >> CRYST1   30.000   30.000   30.000  90.00  90.00  90.00 P 1
> >> MODEL1
> >> ATOM  1  CT  ACT 1  14.870  14.744  14.594  1.00  0.00
> >>C
> >> ATOM  2  HC  ACT 1  15.390  13.760  14.594  1.00  0.00
> >>H
> >> ATOM  3  HC  ACT 1  13.769  14.581  14.594  1.00  0.00
> >>H
> >> ATOM  4  HC  ACT 1  15.162  15.317  13.685  1.00  0.00
> >>H
> >> ATOM  5  CZ  ACT 1  15.253  15.501  15.794  1.00  0.00
> >>C
> >> ATOM  6  NZ  ACT 1  15.555  16.097  16.740  1.00  0.00
> >>N
> >> TER
> >> ENDMDL
> >>
> >> The output, however, is this:
> >>
> >> TITLE Great Red Owns Many ACres of Sand
> >> REMARKTHIS IS A SIMULATION BOX
> >> CRYST1   30.000   30.000   30.000  90.00  90.00  90.00 P 1   1
> >> MODEL1
> >> ATOM  1  1CT 1  15.013  15.013  14.819  1.00  0.00
> >>C
> >> ATOM  2  1HC 1  14.952  13.831  14.385  1.00  0.00
> >>H
> >> ATOM  3  1HC 1  13.827  14.934  14.400  1.00  0.00
> >>H
> >> ATOM  4  1HC 1  15.140  15.157  13.573  1.00  0.00
> >>H
> >> ATOM  5  2CZ 1  15.821  15.819  16.308  1.00  0.00
> >>C
> >> ATOM  6  2NZ 1  16.401  16.397  17.446  1.00  0.00
> >>N
> >> TER
> >> ENDMDL
> >>
> >> Why? I don't think I've seen this happen before, and I'd like to keep
> the
> >> initial format. Any suggestions? My itp is for an ACT residue, which is
> >> included in the simulation topology input.
> >>
> >>
> > mdrun gets the residue and atom names from the topology, so a dump of the
> > .tpr should show something useful.  It seems like something in the
> topology
> > has gotten broken - atom names becoming numbers, residue name becoming
> the
> > atom names.  Bizarre.  grompp should have complained loudly if there were
> > mismatches between coordinates and topology.
> >
> > -Justin
> >
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/Support
> > /Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] output pdb reformatted

2017-07-11 Thread Alex

You are absolutely right once again. I've been glancing over that topology,
looking right at what the problem was, and not seeing it. The residue name
column was empty, all atom types went to crap, but because I always grompp
with -maxwarn 10 (for completely unrelated warnings in completely different
simulations) everything seemed okay.

Thanks!

Alex

On Tue, Jul 11, 2017 at 2:40 PM, Justin Lemkul  wrote:

>
>
> On 7/11/17 4:01 PM, Alex wrote:
>
>> Hi all,
>>
>> I have a tiny acetonitrile molecule here. The input pdb prior to EM is
>> this:
>>
>> TITLE Gromacs Runs On Most of All Computer Systems
>> REMARKTHIS IS A SIMULATION BOX
>> CRYST1   30.000   30.000   30.000  90.00  90.00  90.00 P 1
>> MODEL1
>> ATOM  1  CT  ACT 1  14.870  14.744  14.594  1.00  0.00
>>C
>> ATOM  2  HC  ACT 1  15.390  13.760  14.594  1.00  0.00
>>H
>> ATOM  3  HC  ACT 1  13.769  14.581  14.594  1.00  0.00
>>H
>> ATOM  4  HC  ACT 1  15.162  15.317  13.685  1.00  0.00
>>H
>> ATOM  5  CZ  ACT 1  15.253  15.501  15.794  1.00  0.00
>>C
>> ATOM  6  NZ  ACT 1  15.555  16.097  16.740  1.00  0.00
>>N
>> TER
>> ENDMDL
>>
>> The output, however, is this:
>>
>> TITLE Great Red Owns Many ACres of Sand
>> REMARKTHIS IS A SIMULATION BOX
>> CRYST1   30.000   30.000   30.000  90.00  90.00  90.00 P 1   1
>> MODEL1
>> ATOM  1  1CT 1  15.013  15.013  14.819  1.00  0.00
>>C
>> ATOM  2  1HC 1  14.952  13.831  14.385  1.00  0.00
>>H
>> ATOM  3  1HC 1  13.827  14.934  14.400  1.00  0.00
>>H
>> ATOM  4  1HC 1  15.140  15.157  13.573  1.00  0.00
>>H
>> ATOM  5  2CZ 1  15.821  15.819  16.308  1.00  0.00
>>C
>> ATOM  6  2NZ 1  16.401  16.397  17.446  1.00  0.00
>>N
>> TER
>> ENDMDL
>>
>> Why? I don't think I've seen this happen before, and I'd like to keep the
>> initial format. Any suggestions? My itp is for an ACT residue, which is
>> included in the simulation topology input.
>>
>>
> mdrun gets the residue and atom names from the topology, so a dump of the
> .tpr should show something useful.  It seems like something in the topology
> has gotten broken - atom names becoming numbers, residue name becoming the
> atom names.  Bizarre.  grompp should have complained loudly if there were
> mismatches between coordinates and topology.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
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Re: [gmx-users] output pdb reformatted

2017-07-11 Thread Justin Lemkul




On 7/11/17 4:01 PM, Alex wrote:

Hi all,

I have a tiny acetonitrile molecule here. The input pdb prior to EM is this:

TITLE Gromacs Runs On Most of All Computer Systems
REMARKTHIS IS A SIMULATION BOX
CRYST1   30.000   30.000   30.000  90.00  90.00  90.00 P 1
MODEL1
ATOM  1  CT  ACT 1  14.870  14.744  14.594  1.00  0.00
   C
ATOM  2  HC  ACT 1  15.390  13.760  14.594  1.00  0.00
   H
ATOM  3  HC  ACT 1  13.769  14.581  14.594  1.00  0.00
   H
ATOM  4  HC  ACT 1  15.162  15.317  13.685  1.00  0.00
   H
ATOM  5  CZ  ACT 1  15.253  15.501  15.794  1.00  0.00
   C
ATOM  6  NZ  ACT 1  15.555  16.097  16.740  1.00  0.00
   N
TER
ENDMDL

The output, however, is this:

TITLE Great Red Owns Many ACres of Sand
REMARKTHIS IS A SIMULATION BOX
CRYST1   30.000   30.000   30.000  90.00  90.00  90.00 P 1   1
MODEL1
ATOM  1  1CT 1  15.013  15.013  14.819  1.00  0.00
   C
ATOM  2  1HC 1  14.952  13.831  14.385  1.00  0.00
   H
ATOM  3  1HC 1  13.827  14.934  14.400  1.00  0.00
   H
ATOM  4  1HC 1  15.140  15.157  13.573  1.00  0.00
   H
ATOM  5  2CZ 1  15.821  15.819  16.308  1.00  0.00
   C
ATOM  6  2NZ 1  16.401  16.397  17.446  1.00  0.00
   N
TER
ENDMDL

Why? I don't think I've seen this happen before, and I'd like to keep the
initial format. Any suggestions? My itp is for an ACT residue, which is
included in the simulation topology input.



mdrun gets the residue and atom names from the topology, so a dump of the .tpr 
should show something useful.  It seems like something in the topology has 
gotten broken - atom names becoming numbers, residue name becoming the atom 
names.  Bizarre.  grompp should have complained loudly if there were mismatches 
between coordinates and topology.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
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* Please search the archive at 
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[gmx-users] output pdb reformatted

2017-07-11 Thread Alex

Hi all,

I have a tiny acetonitrile molecule here. The input pdb prior to EM is this:

TITLE Gromacs Runs On Most of All Computer Systems
REMARKTHIS IS A SIMULATION BOX
CRYST1   30.000   30.000   30.000  90.00  90.00  90.00 P 1
MODEL1
ATOM  1  CT  ACT 1  14.870  14.744  14.594  1.00  0.00
  C
ATOM  2  HC  ACT 1  15.390  13.760  14.594  1.00  0.00
  H
ATOM  3  HC  ACT 1  13.769  14.581  14.594  1.00  0.00
  H
ATOM  4  HC  ACT 1  15.162  15.317  13.685  1.00  0.00
  H
ATOM  5  CZ  ACT 1  15.253  15.501  15.794  1.00  0.00
  C
ATOM  6  NZ  ACT 1  15.555  16.097  16.740  1.00  0.00
  N
TER
ENDMDL

The output, however, is this:

TITLE Great Red Owns Many ACres of Sand
REMARKTHIS IS A SIMULATION BOX
CRYST1   30.000   30.000   30.000  90.00  90.00  90.00 P 1   1
MODEL1
ATOM  1  1CT 1  15.013  15.013  14.819  1.00  0.00
  C
ATOM  2  1HC 1  14.952  13.831  14.385  1.00  0.00
  H
ATOM  3  1HC 1  13.827  14.934  14.400  1.00  0.00
  H
ATOM  4  1HC 1  15.140  15.157  13.573  1.00  0.00
  H
ATOM  5  2CZ 1  15.821  15.819  16.308  1.00  0.00
  C
ATOM  6  2NZ 1  16.401  16.397  17.446  1.00  0.00
  N
TER
ENDMDL

Why? I don't think I've seen this happen before, and I'd like to keep the
initial format. Any suggestions? My itp is for an ACT residue, which is
included in the simulation topology input.

Thank you,

Alex
-- 
Gromacs Users mailing list

* Please search the archive at 
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Re: [gmx-users] output pdb reformatted

Re: [gmx-users] output pdb reformatted

Re: [gmx-users] output pdb reformatted

[gmx-users] output pdb reformatted

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