On 3/3/14, 3:56 PM, gromacs query wrote:
What atom numbers are on line 184419? What atom types are they in the
[atoms] section for that [moleculetype]?
These are waters only (I am using tipS3p CHARMM TIP3P). UB should not be
there. I am following Justin's suggestion to remove moleculetype from top
file (still not solved and trying, will let you know; I am newbie to
gromacs)
Hopefully you're not removing entire [moleculetype] directives, that would be
rather horrible.
The proper solution is to not process waters with pdb2gmx. You can hack the
topology to fix it, but the best bet is to strip waters, process with pdb2gmx to
get a topology for everything that's not water, then add back the water
coordinates from the original coordinate file and adjust [molecules]
accordingly. If you are very new to Gromacs, invest some time working with
tutorials simple systems to familiarize yourself with the format before doing
these manipulations. In the long run, it will save you time and mistakes.
-Justin
thanks
On Mon, Mar 3, 2014 at 6:48 PM, Mark Abraham <[email protected]>wrote:
On Mon, Mar 3, 2014 at 7:25 PM, gromacs query <[email protected]
wrote:
Hi Justin
Its problem with the waters I think.
Can't be, they have no U-B.
I found conflict in water atom names:
charmm36-jan2014.ff/tip3p.itp:
1 OT 1 SOL OW 1 -0.834
2 HT 1 SOL HW1 1 0.417
3 HT 1 SOL HW2 1 0.417
charmm36-jan2014.ff/merged.itp
[ TIP3 ]
[ atoms ]
OH2 OT -0.834 0
H1 HT 0.417 1
H2 HT 0.417 2
In PDB from charmgui its OH2,H1,H2. I changed names in
charmm36-jan2014.ff/tip3p.itp as in merged.rtp but still I get same
error.
On Mon, Mar 3, 2014 at 5:46 PM, Justin Lemkul <[email protected]> wrote:
On 3/3/14, 10:57 AM, gromacs query wrote:
Hi All
I am trying to use charmm36 (charmm36-jan2014 from charmm website)
with
popc membrane built using charmm-gui (have water and ions).
I used commands as follows:
pdb2gmx -f step5_assembly.pdb -o popc.gro -water tip3p -ff
charmm36-jan2014
editconf -f popc.gro -o popc_box.gro -c -d 0.0
grompp -f minim.mdp -c popc_box.gro -p topol.top -o em.tpr
I get this error: (so many)
ERROR 11520 [file topol.top, line 184419]:
No default U-B types
What atom numbers are on line 184419? What atom types are they in the
[atoms] section for that [moleculetype]?
Mark
Where are UB for charmm36?
This shouldn't happen. Can you please identify what atoms are causing
the
failure? It may help to simplify by working only with a single lipid
rather than a full membrane.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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