On 4/1/16 4:31 AM, bio hpc wrote:
Did anybody of you wrote such script or can that be found in some repository?
The specifics depend on the input file itself, and different programs write
different names (an unfortunate truth that not everyone sticks to IUPAC/IUPAB
nomenclature), and sometimes force fields have their own quirks. It's just a
listing of sed commands based on each residue. But the easiest way has already
been suggested: use -ignh and specify protonation states when running pdb2gmx.
The initial H coordinates themselves are going to change as soon as you run
energy minimization, so preserving these exact coordinates has no bearing on
anything of importance. Key interactions will be preserved only if the force
field represents them correctly, which is another issue entirely.
-Justin
El 31/3/2016, a las 13:04, Justin Lemkul <jalem...@vt.edu> escribió:
On 3/31/16 6:55 AM, bio hpc wrote:
Thanks.
Apart from this, is is there some script that keeps my original hydrogens from
Maestro?
Rename with sed according to what the force field expects.
-Justin
El 30/3/2016, a las 19:43, Tsjerk Wassenaar <tsje...@gmail.com> escribió:
Hey :)
-ignh does ignore the hydrogens in the input file. It builds those
hydrogens that are specified in the force field. For histidines, the
protonation state is determined from the possible hydrogen-bonded network,
but it is possible to assign specific states interactively, using the
option -his, or by specifying the residue name in the input file.
Hope it helps,
Tsjerk
On Wed, Mar 30, 2016 at 4:42 PM, sun <sun.i...@gmail.com> wrote:
I think using -ignh does not "remove" hydrogens. Hence, you can use it.
Sent from my iPhone
On 30-Mar-2016, at 6:04 pm, rajendra kumar <rjd...@gmail.com> wrote:
Hi,
As suggested above, use -ignh to ignore hydrogen atoms. To use a specific
Histidine, you may change residue name HIS to
HIP(Amber)/HSP(Charmm)/HISH(
OPLS
) or HID(Amber)/HSD(Charmm)/HISD(
OPLS
) or HIE(Amber)/HSE(Charmm)/HISE(
OPLS
) either in PDB file or interactively through pdb2gmx usng -his command.
On Wed, Mar 30, 2016 at 12:27 PM, bio hpc <biohpc2...@gmail.com> wrote:
Hi,
we have created some protein pdb files with Maestro. When we try to un
an
MD simulation with gromacs, we get errors like:
Atom HD11 in residue ASN 5 was not found in rtp entry ASN with 14
atoms
I tried to find a solution and it seems that internal gromacs dictionary
for hydrogens is different from the one from Maestro and other formats.
It
seems, from what I read, that one must convert all hydrogen types to
Gromacs format. Is is there any script that can do this automatically?
Of course, there is the option “ignore hydrogens”, but this would be bad
for us, since we need some histidines in the binding site, and so on.
Thanks,
BIO-HPC
--
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!
* 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!
* 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.
--
Tsjerk A. Wassenaar, Ph.D.
--
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.
--
==================================================
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.
--
==================================================
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.
