Dear AMBER users,
I have been encountering an issue when trying to use charmmlipid4amber.py module. I was able to convert the POPC molecules into AMBER format, however I am encountering an issue with converting water molecules. I suspect because when I built the system on CHARMM-GUI, it had added water molecules that are not the type presented in charmmlipd4amber.csv.
I have attached a sample of the PDB for the water molecules below;
PDB for water molecules:
ATOM 3010 OH2 TIP3 10007 -46.839 11.708 31.737 1.00 0.00 TIP3 O
ATOM 3011 H1 TIP3 10007 -47.079 12.370 32.385 1.00 0.00 TIP3 H
ATOM 3012 H2 TIP3 10007 -47.037 10.873 32.162 1.00 0.00 TIP3 H
ATOM 3013 H1 TIP3 10008 -52.579 11.386 36.175 1.00 0.00 TIP3 H
ATOM 3014 H2 TIP3 10008 -52.918 10.450 35.034 1.00 0.00 TIP3 H
ATOM 3015 OH2 TIP3 10009 -46.289 5.967 23.172 1.00 0.00 TIP3 O
ATOM 3016 H1 TIP3 10009 -45.709 6.117 23.919 1.00 0.00 TIP3 H
ATOM 3017 H2 TIP3 10009 -45.875 6.438 22.449 1.00 0.00 TIP3 H
ATOM 3018 OH2 TIP3 10000 -59.629 71.413 -74.908 1.00 0.00 TIP3 O
ATOM 3019 OH2 TIP3 10000 -60.066 70.980 -71.986 1.00 0.00 TIP3 O
ATOM 3020 OH2 TIP3 10000 -61.615 66.770 -67.348 1.00 0.00 TIP3 O
ATOM 3021 OH2 TIP3 10000 -60.314 65.026 -81.834 1.00 0.00 TIP3 O
ATOM 3022 OH2 TIP3 10000 -59.919 63.080 -80.011 1.00 0.00 TIP3 O
ATOM 3023 OH2 TIP3 10000 -60.160 65.865 -75.063 1.00 0.00 TIP3 O
ATOM 3024 OH2 TIP3 10000 -61.674 68.742 -72.756 1.00 0.00 TIP3 O
ATOM 3025 OH2 TIP3 10000 -59.651 62.981 -83.619 1.00 0.00 TIP3 O
ATOM 3026 OH2 TIP3 10000 -61.302 60.220 -85.069 1.00 0.00 TIP3 O
ATOM 3027 OH2 TIP3 10000 -62.133 61.601 -79.448 1.00 0.00 TIP3 O
ATOM 3028 H1 TIP3 10000 -47.811 5.076 22.225 1.00 0.00 TIP3 H
ATOM 3029 H2 TIP3 10000 -48.209 4.425 20.918 1.00 0.00 TIP3 H
ATOM 3030 OH2 TIP3 10001 -41.196 5.974 32.829 1.00 0.00 TIP3 O
ATOM 3031 H1 TIP3 10001 -41.849 6.668 32.918 1.00 0.00 TIP3 H
ATOM 3032 H2 TIP3 10001 -40.731 6.184 32.019 1.00 0.00 TIP3 H
ATOM 3033 OH2 TIP3 10002 -45.160 6.805 25.487 1.00 0.00 TIP3 O
ATOM 3034 H1 TIP3 10002 -45.892 7.034 26.060 1.00 0.00 TIP3 H
ATOM 3035 H2 TIP3 10002 -44.713 6.091 25.942 1.00 0.00 TIP3 H
ATOM 3036 OH2 TIP3 10003 -45.263 4.979 34.554 1.00 0.00 TIP3 O
ATOM 3037 H2 TIP3 10003 -45.864 5.259 33.864 1.00 0.00 TIP3 H
ATOM 3038 H1 TIP3 10004 -53.845 7.065 26.551 1.00 0.00 TIP3 H
ATOM 3039 H1 TIP3 10005 -52.243 10.285 29.294 1.00 0.00 TIP3 H
ATOM 3040 OH2 TIP3 10008 -52.268 10.604 35.720 1.00 0.00 TIP3 O
ATOM 3041 H1 TIP3 10000 -59.650 71.598 -73.969 1.00 0.00 TIP3 H
ATOM 3042 H1 TIP3 10000 -60.553 70.244 -72.358 1.00 0.00 TIP3 H
ATOM 3043 H1 TIP3 10000 -62.481 66.665 -66.954 1.00 0.00 TIP3 H
How can I resolve this issue?
Thank you,
Sincerely,
Kav
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Received on Wed Jun 19 2024 - 12:00:02 PDT
