GROMACS version: 2022.4
GROMACS modification: No
Hey,
I was wondering if ParmEd is now capable of converting an amber topology with ff19SB cmap parameters to a GROMACS topology.
I generated the AMBER topology using tleap. This assigned the CA-atoms the atomtype XC. I used the AMBER 2022 for tleap and ParmEd.
When I converted the AMBER topology to a GROMACS topology using ParmEd it added [cmaptypes] to the GROMACS topology.
However, I compared the [cmaptypes] values generated by ParmEd with the values from CHARMM-GUI and noticed a significant difference.
CHARMM-GUI assigned 14 different XC atomtypes (XC0 until XC13) and assigned different [cmaptypes] for every single XC atomtype.
Are the cmaptypes generated by ParmEd different from the ones generated by CHARMM-GUI?
I know that this is more an AMBER related question but I thought this might help others using the AMBER force field with ff19SB for GROMACS.
I posted this question also on github CMAPTYPES are differnt when converting Amber topology generated by tleap with ff19SB to a GROMACS topology using ParmEd compared to CHARMM-GUI · Issue #1292 · ParmEd/ParmEd · GitHub .
@jalemkul suggested here Amber ff19sb - #6 by michael.brunsteiner hat CHARMM-GUI generates an accurate topology file for GROMACS with ff19SB. I was just wondering if ParmEd also generates an accurate topology file for GROMACS.
This is the atomtype generated by ParmEd:
XC 6 12.010000 0.00000000 A 0.33996695 0.4577296
These are the the [cmaptypes] generated by ParmEd:
[ cmaptypes ]
C N XC C N 1 24 24\
-3.62727696 -1.1221906400000001 0.49802152 1.51699288 3.99877432 7.00723768 10.17364704 10.893671600000001 9.50621536 7.55684792\
6.1457102400000005 6.745988720000001 -4.04437992 -6.266376800000001 -4.52871976 -0.41727032000000003 2.8618560000000004 4.10320696 3.12841864 0.8612764\
-1.86719368 -3.9567669600000004 -4.4959172 -4.339226399999999 -1.36590864 0.7804833600000001 2.5678044800000004 2.80729664 4.23855936 7.069202720000001\
10.839237760000001 11.2708592 10.99182824 9.5526996 6.521768160000001 -0.5083141600000001 -5.0996684000000005 -6.04265832 -4.05852184 -0.22463896000000003\
3.3805046400000003 4.72097456 3.52117072 1.7380336 -0.23505712 -2.02225272 -2.39504712 -2.05091312 -0.011296800000000001 1.85556216\
2.8334048000000003 2.92490888 4.02074032 6.35244168 9.70361648 10.86860944 10.3267396 8.7880736 4.24650896 -1.4701739200000001\
-4.438303520000001 -2.14969736 -2.8896377600000003 0.5608652000000001 3.9649257600000003 5.23184096 4.43068864 2.96256488 5.3536372 0.019999520000000003\
-0.62178424 -0.55224616 1.95698232 4.440144480000001 3.5208778400000003 3.6535106400000004 6.42566168 9.48583928 9.555377360000001 10.94254072\
10.38983432 8.78899408 4.17931392 -0.67847744 -2.96758568 -2.95612152 -1.2261212 1.7093732000000001 5.07284896 6.605615520000001\
6.10667352 4.8239009600000005 3.09582528 1.8756872 2.17095208 1.78414128 4.52976576 5.10581888 4.243914880000001 3.8862247200000004\
5.01146968 7.94579256 11.02555128 12.216819760000002 11.358848720000001 9.02539008 4.7643208 0.4589848 -1.4777469600000002 -1.906858\
-0.30601775999999997 2.9997606400000003 5.85479672 7.1207496 7.38944608 6.46858952 5.39346888 4.02362728 4.41801112 4.1792720800000005\
5.39259024 4.548802960000001 5.25129656 2.5917787999999997 4.4973816 8.10687656 13.355620880000002 12.782161839999999 11.92540416 9.42353952\
5.391293200000001 1.2685469600000001 -1.3631472 -1.41979856 3.9467672000000005 4.24219944 5.721285280000001 6.50185232 7.04129544 7.108741520000001\
6.64745552 5.676432800000001 5.78090728 5.81509056 4.1204868800000005 3.2255292800000004 2.43897912 3.14862736 5.57128888 9.16689296\
12.44158424 13.871215200000002 12.479240240000001 9.798133040000002 7.03698592 0.8727824000000001 -0.7916128 0.6329973600000001 4.07299848 4.95544592\
5.9030800800000005 9.132123920000002 7.28367456 7.69759768 10.43226008 5.890318880000001 5.43384448 5.1559432 2.0290308 2.1495300000000004\
3.01741712 4.85641064 8.51510944 11.5513964 13.965397040000001 13.96259376 13.46750104 8.00600032 2.99800336 -0.25300648000000003\
0.23940848 3.99567816 6.58825192 8.27787664 9.23279096 9.445505520000001 9.0474816 8.58063088 6.1227819199999995 3.88120392\
2.675668 2.1950937600000002 0.33279536 1.8694112 4.28542016 8.45234944 12.5204108 15.60744968 16.35404264 14.0695368\
9.831563200000002 5.0787065600000005 1.32532384 0.9313165600000001 3.63999632 7.28087128 11.111658 10.724177760000002 12.33635664 12.752832000000001\
12.232426080000002 10.621418720000001 6.401854720000001 1.8409600000000002 0.0 -0.03217496 1.04570712 4.581145279999999 9.103003280000001 14.35664288\
18.85168144 21.15823696 19.43660464 14.679480320000001 9.01204312 5.333093760000001 4.06019544 5.6478560799999995 8.841754320000001 9.64612832\
10.73961672 13.06173672 15.548413440000001 17.39033576 16.820474960000002 13.02818104 6.30537168 2.1719980800000003 -0.8449588 -0.36045160000000004\
6.40059952 11.81440264 17.240674079999998 21.317061600000002 25.75703872 25.44608384 21.06313464 14.752658480000001 9.83068456 9.142625760000001\
10.23954504 11.94109416 11.060236640000001 10.12871088 11.3685556 15.408123920000001 20.05608768 23.711774000000002 21.26045208 13.35327784\
5.621162160000001 1.04775728 1.5361556 3.4707953600000003 14.63885368 21.35634936 20.09495704 19.02259784 19.61057536 19.501540320000004\
18.311819919999998 15.41230792 14.206144400000001 16.54847312 16.5784724 11.963311200000001 9.25701632 9.22375352 10.616314240000001 18.04960864\
23.1002824 19.64873344 15.8471092 10.93798016 6.37060024 5.64915312 7.324008320000001 10.61510088 23.66813488 17.37485496\
14.025981360000001 12.56292024 12.90764 14.833242320000002 17.424686400000002 19.364932720000002 21.49651336 20.96924568 12.63793936 6.1544966400000005\
5.72848176 5.70827304 12.22401624 25.46729672 15.862548160000001 13.677537840000001 16.21835552 13.18537392 10.73555824 12.40317512\
14.72876784 20.2089292 19.02473168 12.99521112 9.043548640000001 7.49383688 8.82288448 14.551784640000001 20.400932960000002 24.79543\
25.18123664 17.258288720000003 9.510817760000002 7.749186400000001 5.8870971999999995 9.68905616 15.191392720000001 13.73808032 10.392846800000001 10.104945760000001\
12.267906400000001 14.922821760000001 16.034343200000002 17.283183519999998 19.3265236 21.798640000000002 10.64422152 7.06895168 4.08027864 3.69919992\
8.4797128 16.819596320000002 24.39811736 27.17085416 22.82376184 16.875829279999998 11.42152504 12.728522960000001 10.199085760000001 12.45099824\
11.43541592 7.25417736 6.5109316 9.627886080000001 16.17772888 18.267343999999998 19.15213448 20.01257408 19.340581840000002 15.28544904\
5.81969296 3.3777432000000003 1.2292592 2.2449252 8.96744168 18.215629760000002 23.60453808 23.132122640000002 20.13453768 16.29559216\
12.641453920000002 10.75124824 9.91202152 8.0320248 4.375794560000001 2.57918496 5.30271792 10.376696560000001 14.6992288 17.36138248\
16.666964 15.042023920000002 12.3764812 8.58293208 2.48809928 1.11721168 -0.004937120000000001 1.4367019200000002 8.18260696 15.53443888\
18.05554992 17.861579680000002 16.45910288 15.91317456 10.25130208 7.56337496 5.1666124 1.20114272 -0.6919917600000001 0.47731072\
4.63972128 9.07672776 13.705235920000002 12.16050312 11.156008400000001 9.73169112 6.832932240000001 4.3652508800000005 -0.004225840000000001 -0.30451152\
-0.63797632 1.6709222400000001 5.668357680000001 10.82384064 12.06766016 12.214016480000002 11.259897120000002 8.734183680000001 5.4525051200000005 2.25605464\
-1.9681536 -4.42198592 -3.52916216 0.3135908 4.749174720000001 7.99022664 6.71046656 6.36223224 4.99084256 3.45715552\
2.07911328 0.78445816 2.2030015200000004 -0.04673528 0.048952800000000005 1.46519496 4.15086272 7.03125384 7.7464668 7.172003600000001\
5.805467360000001 3.80907176 1.0377993600000002 -3.08356616 -6.320726960000001 -6.44181192 -3.02097352 1.803304 4.9382078400000005 5.1802104\
4.0719106400000005 2.908926 1.2304725600000002 -0.17643928 -0.53086592 -0.75634168 1.7463179199999999 1.7920072 1.0625268 1.7434728000000002\
3.5440572 6.45917552 7.959725280000001 7.33994936 5.83496456 3.6806648 -0.8266747200000001 -5.00665808 -6.935607600000001 -5.923749040000001\
-2.3894824000000003 2.4081012 5.44593624 5.770196240000001 4.82461224 3.0583366400000003 0.7710275200000001 0.49965328000000003 0.503126 0.9700604\
2.13618304 1.99857128 1.26938376 1.6630563200000001 3.5384088 6.49888168 9.5832428 9.998086400000002 8.04503704 4.42261352\
1.4160329600000001 -3.95760376 -5.888310560000001 -5.11565128 -1.18808864 3.83229296 5.97847576 6.1747472000000005 5.65580568 5.748648640000001\
2.2264737599999997 2.25509232 2.5727416 2.6965879999999998 -1.0360002400000001 -1.34833584 -0.8304821600000001 -0.3759324 4.26755448 5.8818672\
9.232330720000002 10.4721336 8.02817552 3.50866056 -0.890146 -4.10232832 -6.05219784 -5.01331064 0.03635896 5.25020872\
5.993287120000001 6.964100640000001 6.8447311200000005 3.6463560000000004 2.2255532799999997 1.62535848 1.33063752 0.24547528000000002 -2.12283608 -6.08198792\
-3.3133096 0.48500928 0.9934071200000001 5.313972880000001 9.3232072 14.35187312 8.53498344 3.47196688 -1.18005536 -1.28515744\
-5.35962032 -1.98263024 3.72664696 4.53010048 4.974776 5.44438816 5.049795120000001 3.7840514400000003 1.99497304 -0.7250872\
-2.61809616 -4.54897032 -6.7887492 -8.20633024 -3.51175672 -2.73658704 0.49488352 5.96738816 10.6323808 12.15230248\
9.406719840000001 7.803369200000001 -0.7920312 -3.5868595200000004 -3.66907512 -4.43508184 -4.86544808 1.95878144 1.6382452 7.55705712\
4.78034552 3.33803704 0.20539256 -1.69443632 -5.32882608 -5.7168084
These are the atomtypes generated by CHARMM-GUI
XC0 6 12.0100 -0.003 A 3.39966950842e-01 4.577296e-01
XC1 6 12.0100 -0.003 A 3.39966950842e-01 4.577296e-01
XC2 6 12.0100 -0.003 A 3.39966950842e-01 4.577296e-01
XC3 6 12.0100 -0.003 A 3.39966950842e-01 4.577296e-01
XC4 6 12.0100 -0.003 A 3.39966950842e-01 4.577296e-01
XC5 6 12.0100 -0.003 A 3.39966950842e-01 4.577296e-01
XC6 6 12.0100 -0.003 A 3.39966950842e-01 4.577296e-01
XC7 6 12.0100 -0.003 A 3.39966950842e-01 4.577296e-01
XC8 6 12.0100 -0.003 A 3.39966950842e-01 4.577296e-01
XC9 6 12.0100 -0.003 A 3.39966950842e-01 4.577296e-01
XC10 6 12.0100 -0.003 A 3.39966950842e-01 4.577296e-01
XC11 6 12.0100 -0.003 A 3.39966950842e-01 4.577296e-01
XC12 6 12.0100 -0.003 A 3.39966950842e-01 4.577296e-01
XC13 6 12.0100 -0.003 A 3.39966950842e-01 4.577296e-01